UARTZ ALLEY NDIAN RESERVATION COMMENTS ON PUBLIC … › ~hoopa › LostRiverTMDL.pdf · the...

Quartz Valley Indian Reservation 13601 Quartz Valley Road

Fort Jones, CA 96032 ph: 530-468-5907 fax: 530-468-5908

August 20, 2009 Katharine Carter North Coast Regional Water Quality Control Board 5550 Skylane Blvd. Suite A Santa Rosa, CA 95403 Re: Comments on Public Review Draft, Staff Report for the Klamath River Total

Maximum Daily Loads (TMDLs) and Action Plan Addressing Temperature, Dissolved Oxygen, Nutrient and Microcystin Impairments in California

Dear Ms Carter, The Quartz Valley Indian Community (QVIC) would like to thank the Regional Water Quality Control Board for all the time and effort that has gone into the development of the Klamath TMDL. A healthy Klamath River is necessary for proper ecological function of the cold-water fishery in the basin, the most valued cultural resource of the tribe. Specifically in the Scott and Shasta River basin, due to the distance from the ocean, salmonid populations are extremely dependant on the Klamath River meeting the water quality objectives necessary for migration. It is for these reasons that the QVIC has a great interest in the development, implementation and hopeful attainment of the Klamath River TMDL. We have reviewed the document and offer our comments in an effort to refine the specifics of the Klamath TMDL so that the goals of implementation will be reached. We thank you for this opportunity to provide you with our comments. Sincerely, Crystal Bowman Environmental Director

___________________________________________________________________________________________ QUARTZ VALLEY INDIAN RESERVATION - COMMENTS ON PUBLIC REVIEW DRAFT, STAFF REPORT, KLAMATH RIVER TMDL AND ACTION PLAN, AUGUST 2009

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INTRODUCTION/SUMMARY The Public Review Draft, Staff Report for the Klamath River Total Maximum Daily Loads (TMDLs) and Action Plan Addressing Temperature, Dissolved Oxygen, Nutrient and Microcystin Impairments in California (Public Draft TMDL) was issued by the North Coast Regional Water Quality Control Board in June 2009. The Quartz Valley Tribe has been engaged in the Klamath TMDL process since 2004, and has reviewed a long list of TMDL-related documents in that time, with the help of our consultants. The Agency Review Draft in July 2008 was previously reviewed and the Quartz Valley Tribe submitted comments in September 2008. For the most part it appears that Regional Board staff has incorporated the technical recommendations advanced by the tribe in September 2008; however, some previous comments are repeated here because they are not adequately addressed in the present document. Overall the technical analysis presented in the Klamath TMDL is scientifically rigorous and provides a solid foundation for remediation of the river’s pollution problems. We commend Regional Board Staff for their effort on the TMDL conceptual framework and technical analysis. The Implementation Plan (Chapter 6 of the Public Draft TMDL), the most important part of the TMDL from a practical perspective, was released on June 30. Overall, we are cautiously optimistic – with some specific reservations – about this plan: - The Public Draft TMDL would require PacifiCorp to propose an implementation

plan for approval by the Regional Water Board that includes implementation measures, a timeline for implementation, measurable milestones, and a requirement to update the plan periodically. In our opinion, the only way that PacifiCorp can meet TMDL requirements (particularly for temperature) is to remove its California reservoirs.

- Irrigated agriculture in the California portion of the Lost River is included in the implementation plan, which is a positive step. Previously, Regional Board Staff was undecided whether Lost River would be included in the implementation plan.

- Strong protections for thermal refugia are proposed, including the prohibition of waste discharge (e.g. suction dredge mining) . We have included additional data for protection of critical thermal refuge habitat in the Scott River.

- The proposed watershed-wide protections for riparian shade and class III (ephemeral) streams concerning private land timber harvest are necessary and good.

- The proposed approach for developing a conditional waiver of waste discharge covering all activities for each National Forest in the Klamath Basin makes sense, but we withhold judgment until more details on the proposed waivers are available.

- The proposed Klamath River water quality accounting and tracking program referred to as “KlamTrack” (previously described as “pollutant trading”) offers promise for cost-effective water quality improvements, but only if properly implemented. One shortcoming of the proposed KlamTrack Program is lack of specific mention of Tribes in the development of the program.


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Reservations we have regarding the implementation plan are: - Pollutant reductions in Oregon are key to the successful reduction of nutrient

concentrations in California downstream, yet Oregon’s authority to regulate non-point source discharges (i.e. irrigation tailwater return flow) is weak. We need to know more about the proposed development of a Management Agency Agreement (MAA) between USBR, USFWS and the Regional Water Board to implement the Lost River and Klamath River TMDLs, as well as the MOU between U.S. EPA, Oregon Department of Environmental Water Quality (ODEQ) and the Regional Water Board.

- There are disturbing developments within the State Water Resources Control Board (SWRCB 2009) with regard to a potential shift in oversight authority of U.S. Forest Service activities (QVIR 2009, included here as appendix A).

- Lack of regulation of water use by the SWRCB Water Rights Division (WRD) and other agencies with authority over streamflow flow remains a huge impediment to successful TMDL implementation.

- The proposed approach of continuing the status quo in the Shasta and Scott watersheds is unfortunate, given the acute water quality problems and slow pace of TMDL implementation there.

- Many aspects of the implementation plan look good on paper, such as requirements for farmers to develop water quality management plans, yet it remains to be seen how effective such efforts will actually be in practice.

- Overall, the implementation plan needs to be strengthened, and while maintaining reasonable flexibility for those engaged in good-faith efforts to comply, the plan should more explicit regarding how it will deal with those who would deliberately delay.

It is understandable that implementation of the TMDL will be adaptively managed. However, we request that any revisions made to the implementation plan or timeline be a transparent process with input from the various stakeholders. Likewise, stakeholder input is necessary in the development of polluter MOU’s, waivers (i.e. timber, grazing, irrigated agriculture), KlamTrack, nonpoint and point source control trade-offs. Timely implementation will be critical to the success of the TMDL. Many of the drivers of water problems (e.g. Shasta and Scott River flow depletion, the Klamath Hydroelectric Project, and Upper Klamath Basin agricultural pollution) were identified decades ago, yet positive action has been slow in coming. We strongly encourage the Regional Water Board to fast-track implementation, to the maximum extent possible, of these key problems. The comments below are organized using the same chapter/section numbering system as the Public Draft TMDL. Since Work Group member Tribes have already submitted extensive comments in the past on various aspects of the technical TMDL, we focus the comments here primarily on the Implementation Plan (Chapter 6) and upon aspects of the technical analysis that have changed since the agency review draft.


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DETAILED COMMENTS Chapter 1: Problem Statement General Comments on Chapter 1 The background material on the Klamath Basin and changes in water quality caused by human uses is well researched and clearly stated. For example: “The conversion of wetlands to farmland and other land uses has exposed the nutrient and organic rich soils to oxidation, resulting in the release to the water column of nitrogen and phosphorus previously stored in the soil and wetland vegetation.” (p 1-14) The Public Draft TMDL recognizes that streamflow must be considered, because of its profound impact on water quality, and describes clearly how human use has altered basin flow regimes. One deficiency in the plan is that water use discussions do not mention that groundwater withdrawal can reduce surface flows. Relevant overlapping regulatory processes are clearly described, including Tribal Trust responsibilities: “The California Regional Water Board must consider federal Tribal Trust responsibilities in the Klamath River basin since TMDLs are subject to the approval of the U.S. EPA” (p 1-8). Discussions of Treaty Rights extend not just to fishing but also ceremonial uses of aquatic resources. The document specifically mentions the water quality authority of Tribes and cites all of the completed Tribal water quality plans. Discussions regarding the Klamath Hydroelectric Project (KHP) clearly define the reservoirs as water quality nuisances and note that a SWRCB letter stating that PacifiCorp has not provided evidence demonstrating that the company’s proposal to relicense the KHP will resolve the reservoirs’ water quality impacts and meet requirements for 401 Certification. Chapter 2: Problem Statement The problem statement is well-organized and presents a compelling description of Klamath River water quality problems and the various inter-related causal mechanisms. The first sentence in this chapter is indicative of the inclusive approach taken in the Public Draft TMDL to water quality problems:

“In the Klamath River in California increased water temperatures, elevated nutrient levels, low dissolved oxygen concentrations, elevated pH, potential ammonia toxicity, increased incidence of fish disease, an abundance of aquatic plant growth - high Chlorophyll-a levels (both planktonic and periphytic algae), and high concentrations of potentially toxigenic blue-green algae, particularly in the impounded reaches, decrease the quality and quantity of suitable habitat for fish and aquatic life, and have disrupted traditional cultural uses of the river by resident Tribes. These conditions contribute to the non-attainment of beneficial uses, including the most sensitive beneficial uses: those associated with the cold water fishery (specifically the salmonid fishery) in California, and those related to cultural uses and practices.”


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The TMDL solidly references its selection (U.S. EPA, 2003; Tetra Tech, 2006) of water quality parameters and numeric end-points indicative of pollution and takes an approach generally compatible with the Water Quality Control Plan for the Hoopa Valley Indian Reservation (HVTEPA, 2008). There is an impressive amount of detail on interaction of different water quality problems and their implications for fish health. This includes the recently discovered relationships between nutrient enrichment and the proliferation of the deadly pathogen Ceratomyxa shasta. Two flow charts (Figure 2.7, 2.8) demonstrate the analytical power of graphics in this draft. These figures present pathways for nutrient pollution, including toxigenic algae (Figure 2.7) and relationships of water temperature stress, river ecosystem response, fish physiological response and their impacts on beneficial uses (Figure 2.8)

The amount of data assimilated and interpreted by the Draft Klamath TMDL reflects the huge amount of effort put into the document. Many of the summary charts and maps are innovative and very powerful. Particularly useful examples of such include a temperature summary of Klamath River tributaries (Figure 2.14); a limnological profile of Iron Gate Reservoir (Figure 2.15) showing that areas having temperature and dissolved oxygen suitable for trout do not overlap; charts summarizing exceedance of D.O. (Figure 2.25 and 2.26) and pH (Figure 2.27); and a map of river reaches where fish kills have occurred (Figure 2.29). 2.3.2.2 Suspended Algae Chlorophyll-a, Microcystis aeruginosa, and Microcystin Toxin Section 2.3.2.2 includes recent analyses by Kann and Corum (2009), showing quantitative relationships between chlorophyll, Microcystis, and microcystin (i.e. the probability of exceeding the microcystin target based on a given chlorophyll concentration). These analyses are a welcome addition, providing added support for the TMDL’s in-reservoir chlorophyll targets. [ Note: the final May version of the Kann and Corum (2009) report is available on the Karuk Tribe website, but this Public Draft TMDL cites an outdated January draft version.] 2.5.3.4 Evidence of Water Quality Objective and Numeric Target Exceedances. Nutrients and Indicators of Nutrient-Related Impairment: Chlorophyll-a – Reservoirs While the discussions on page 2-60 notes that the chlorophyll-a target of 10 ug/L is exceeded at reservoir stations in California and Oregon, the text should also note that while the target is not exceeded in the Klamath River between Boyle and Copco Reservoirs, it is exceeded at the below Iron Gate Dam station and at I-5, indicating that Iron Gate Reservoir is releasing algae into the river below it. The following statement on page 2-61 appears to have an erroneous citation: “The reservoirs also impact the river below Iron Gate by serving as a source of blue-green algae that continues to grow in backwater and slower sections within the river reaches below the dams (Kann and Asarian 2005).” This subject was not mentioned in the cited document. A more appropriate citation would be Kann and Corum (2009), already cited elsewhere in the Public Draft TMDL.


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2.5.4 Blue-Green Algae and Microcystin Toxin We could not find any mention in the Public Draft TMDL of the sampling that has been conducted on Klamath River aquatic fauna to assess the concentrations of microcystin in their tissues. This section of the Public Draft TMDL seems to be the most appropriate place for such a discussion, and it could be as simple as: “Bioaccumulation studies in 2007 showed accumulation of microcystin toxin in muscle and/or liver tissues of yellow perch, hatchery salmon, and freshwater mussels (Kann 2008, Mekebri et al. 2009).” In discussing how best to collect samples to assess the potential public health threats posed by blue-green algae, it is noted that “Few samples have been taken in near shore backwater areas where scums have been frequently reported and photographed.” (p. 2-62) Due to a recently-released report, this statement is now outdated and should be replaced with the following language: “Prior to 2008, few samples had been taken in near shore backwater areas where scums have been frequently reported and photographed. In 2008, however, the Karuk Tribe began collecting samples in these areas. These samples frequently show high levels of Microcystis even when mid-channel samples did not (Kann and Corum 2009).” 2.5.5 Evidence of Water Quality Objective and Numeric Target Exceedances: Dissolved Oxygen Data in Figure 2-26 showing frequency of dissolved oxygen saturation less than 85% is credited to the U.S. Fish and Wildlife Service, but this dataset also includes data from the Karuk and Yurok Tribes, and should be cited accordingly. Chapter 3: Analytical Approach General Comments on Chapter 3 This section clearly describes the methods and tools used in the development of the TMDL. 3.2 Modeling Approach The Public Draft TMDL includes outputs from updated water quality model simulations. Previous version of the model outputs presented in last year’s Agency Review Draft (i.e. see Figures 2.9 and 2.10 in that document) included the following patterns that in our opinion appear to be erroneous:

• N and P concentrations remain relatively constant between Iron Gate Dam and the estuary under natural conditions (they should decrease due to dilution and natural river purification processes).

• Natural N concentrations are higher than currently measured N concentrations.

These patterns are no longer present in the new outputs of the Public Draft TMDL (Figures Figure 2.16 and 2.17), indicating that revised boundary conditions (model inputs) for the Shasta, Scott, Salmon, and Trinity Rivers have improved the model’s performance.


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We have not yet been able to examine the most recent model outputs in detail. We expect (though reserve the right to be pleasantly surprised) that when we do obtain and examine the model outputs, they will show that while model performance has improved due to improved boundary conditions, the model will continue to under-represent nutrient reduction in free-flowing river reaches (an issue that Work Group members have been bringing to the attention of the TMDL team for several years now). That said, it is our opinion that on the whole, the model is robust enough to serve its intended purposes in the TMDL (i.e. setting load allocations). It is abundantly clear that the current nutrient concentrations in the river are far higher than natural background and that substantial reductions are necessary to restore water quality. 3.2.2.3 TMDL Compliance: Temperature Compliance in California (TCT1 and TCT2) It is our understanding based on previous inter-agency/inter-Tribal meetings that in the natural conditions (T1BSR) and the temperature compliance in California (TCT1 and TCT2) model scenarios, the small tributaries between Iron Gate Dam and the Klamath River estuary had their temperatures reduced by 2˚C; however, this is not mentioned in this section of the TMDL, nor is there any presentation in Chapter 4 of modeling results indicating what effect this 2˚C decrease had on mainstem temperatures. We discussed this issue with Regional Board Staff on August 6, 2009, and staff confirmed that the 2˚C reduction was included, but had essentially no effect on mainstem Klamath temperatures. The TMDL text in Chapter 3 should be amended to mention the 2˚C reduction, and at least briefly mention the results in Chapter 4. Chapter 4: Pollutant Source Analysis: General Comments on Chapter 4 This chapter is well researched, scientifically solid, and contains useful illustrations (e.g. the conceptual source loading diagrams) that make subjects easily understandable. The sources of pollution in all areas of the Klamath Basin are clearly described, including the Klamath Hydroelectric Project reservoirs, and the data that show levels of pollution are displayed in easy-to-read charts. The introductory paragraph that explains why the Klamath was known as the “river of renewal” succinctly describes the current problem: “source loads have overwhelmed the historic renewal capabilities of the Klamath, leading to its impaired status. The intent of the source analysis is to assess how and what loading scenarios will allow the river once again be restored through its own unique renewal capabilities.” 4.1.1 Pollutant Source Categories This section recognizes and clearly describes the interplay of sediment contributions in Klamath River tributary watersheds and the resulting impacts on water temperature and nutrients. This may obviate the need to develop a separate sediment TMDL; thus, implementation to reduce the risk of cumulative watershed


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effects can begin immediately (rather than waiting for a new sediment TMDL) with the goal of protecting and restoring critical salmonid cold water refugia. The recognition of the importance of refugia, and the description of how they work synergistically within the larger river system to support cold water fisheries, reflects cutting-edge understanding of Klamath River ecology and is in accordance with U.S. EPA (2003) guidance on Pacific salmon, temperature and TMDL development. 4.1.2 Natural Background This section provides useful geologic background information that explains the Klamath River’s lack of buffer capacity and; therefore, its susceptibility to nutrient pollution. We generally agree with the information presented in this section and with its conclusion that:

“These natural background heat, nutrient, and organic matter loads to the Klamath River underscore the very limited capacity of the river to assimilate anthropogenic pollutant sources, and the necessity for establishing load allocations that will result in attainment of water quality standards.” (p. 4-5)

In the discussion regarding historically high ambient air temperatures, it would be good to add a note regarding the historical status of thermal refugia. Prior to widespread logging and agricultural development, which have increased sediment levels, reduced stream canopy, and depleted streamflow, there were likely a greater abundance of high-quality cool-water refugia due to more (and colder) water in tributaries and greater connection with hyporheic flow in the mainstem. U.S. EPA (2003) states that this was generally true for most large rivers in the Pacific Northwest:

“Alluvial floodplains with a high level of groundwater exchange historically provided high quality habitat that served as cold water refugia during the summer for large rivers in the Columbia River basin and other rivers of the Pacific Northwest. These alluvial reaches are interspersed between bedrock canyons and are like beads on a string along the river continuum. Today, most of the alluvial floodplains are either flooded by dams, altered through diking and channelization, or lack sufficient water to function as refugia.”

While much of the length of the Klamath River does flow through canyons, there are many small alluvial features (i.e. gravel bars) in those canyon reaches that should provide some hyporheic flow, particularly in historical conditions prior to the clogging of gravel pore spaces by fine sediments. In addition, there are some significant alluvial valleys including Seiad Valley, Scott Valley, and the areas now impounded under Keno, Copco, and J.C. Boyle Reservoirs. Snyder (1931) made the following observation related to water temperature that suggests hyporheic connection at some locations in the 1920’s:


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“One may at times find a difference of two degrees between the water flowing along the north and south banks where the river is not more than 250 feet across, and where there are neither springs nor tributaries to affect it.”

4.2.2 Pollutant Source Area Loads: Copco 1 and 2 and Iron Gate Reservoirs This section includes a good discussion of how Iron Gate and Copco Reservoirs affect nutrient dynamics, but we have several suggestions for improving it. This section repeatedly refers to May 2004 – May 2005 data from Kann and Asarian (2007), when in fact the data are from May 2005 – May 2006 (this appears to be due to a typographical error in the TetraTech (2008) nutrient dynamics memorandum). Locations requiring correction in section 4.2.2.2 include the caption of Table 4.3 (“May 2004 – May 2005” should be replaced with “May 2005 – May 2006”) and the contents of Table 4.5 (all instances of “2004 – 2005” should be replaced with “2005-2006 May to May”). It should be noted that the data presented from the Asarian and Kann (2009) report are preliminary results, and are subject to revision. It is our understanding that the final numbers will be only slightly different (i.e. within ±1-2%), not enough to affect any conclusions drawn from the data. Hopefully, the Asarian and Kann (2009) report will be completed soon and the final results can be included in the final version of TMDL. In discussing internal nutrient loading, it is stated on page 4-17 that “High pH at the sediment surface may cause release of adsorbed phosphorus from sediments, with or without agitation of sediments.” This sentence should be a candidate for deletion since it may not be relevant to Copco and Iron Gate Reservoirs. In deep portions of the reservoirs, pH is not high at the sediment-water interface, it is close to 7 (see figure 11 from Kann and Asarian 2007). pH is probably (no data exists) high in the margins of the reservoirs where depths are shallow enough for algal photosynthesis to elevate pH. In such cases, however, the water would not be anoxic and we do not know whether high pHs would cause the release of phosphorus from sediments in the presence of oxygen (if yes, then the sentence should stay in; if not, then the sentence should be removed). We are unclear what is meant by the statement “The ~30% export is likely a high estimate because the TMDL model retention does not account for the nitrogen exported downstream within living algal biomass from algae growing within the reservoir and taking up nitrogen from the water column.” (p. 4-19). Is this an artifact of how retention is calculated from the model outputs? If so, is there a better way to calculate it, or is it an inherent characteristic of the model? And, if so, what are its implications for interpreting model outputs? 4.2.3 Pollutant Source Area Loads: Iron Gate Hatchery There appears to be an error in the flow data presented on page 4-21 for various locations associated with Iron Gate Hatchery operations. The calculations used to convert units from millions of gallons per day (mgd) to cubic feet per second (cfs) appear to be


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erroneous, and the cfs numbers require correction. For example, it is erroneously stated that “Average flows through the hatchery system are 16.1 million gallons per day (mgd) (1494.6 cubic feet per second [cfs])”, where the correct number should be 25 cfs (calculation: 16.1 mgd * 1.55 cfs/mgd = 25 cfs). 4.2.4.1 Pollutant Source Area Loads: Shasta and Scott River Temperature A sentence or a small table should be added to indicate how unimpaired flows in the Shasta River compare with current flows. This information is an important product of the TMDL analysis not previously provided, so it should be included somewhere in the TMDL document. The x-axis for Figure 4.17 “Comparison of estimated daily average Scott River Temperature conditions to estimated daily average Klamath River conditions.” is erroneous (discussions with Regional Water Board staff on 8/6/2009 confirmed this) and needs to be corrected. Reducing the number of graphs in this section would make the document shorter and clearer. We suggest that staff consider combining the two Scott River Figures 4.10 and 4.11 together into a single figure with three lines ( likewise, Shasta River Figures 13 and 14 could be combined). Cumulative Temperature Effects of Tributary Inputs and Absence of Impoundments The fall, 2008 Agency Review Draft of the Klamath TMDL included a summary section in Chapter 4 titled “Cumulative Temperature Effects of Tributary Inputs and Absence of Impoundments”; however, this section does not appear in this Public Draft TMDL. The earlier section contained very important information, and should be re-included in the final TMDL. The Klamath TMDL modeling effort has provided excellent information regarding the differences in water temperatures between existing and natural conditions, but some key conclusions resulting from the model outputs should be presented in a more clear and comprehensive fashion. The old Figures 4.21, 4.22, and 4.23 from the Agency Review Draft present some very important information regarding the consequences of Regional Water Board staff’s decision not to require full restoration of flows in the Shasta and Scott Rivers as part of the Klamath TMDL. Because the CA Compliance scenario (used to set the pollutant allocations in Chapter 5) does not require restoration of full natural flows in the Shasta and Scott, maximum temperatures in the Klamath River will still be 1-2˚C warmer than natural in mid-summer (Figure 1). The model results presented in old Figures 4.21, 4.22, and 4.23 show that natural flows in the Shasta and Scott are not necessary to result in near-natural (i.e. <1˚C difference) temperature conditions during the fall chinook spawning (i.e. September-October); the Klamath TMDL’s required mitigation of thermal impacts from the reservoirs (e.g. by dam removal) will be sufficient in that regard. Two points touched on in the previous paragraph should be made clearer in the TMDL ext: t

• Dam removal will result in near-natural temperatures for fall chinook spawning.

• Restoration of natural flows in the Shasta and Scott are required to restore mainstem Klamath summer temperatures for juvenile salmon growth and survival, and the TMDL does not require such restoration of full natural flows

Figure 1. Klamath River 7-day average of daily maximum temperatures downstream of Scott River (Figure 4.23 from the Agency Review Draft of Klamath TMDL) Chapter 5: Klamath River TMDLs – Allocations and Numeric Targets General comments on Chapter 5 This chapter presents pollutant load allocations and numeric targets. The pollutant load allocations are well supported, with one exception, noted below, and, if properly implemented, should result in substantial protection and restoration of beneficial uses. 5.1 Introduction The new table 5.1 in the Public Draft TMDL summarizes all of the numeric targets and allocations, a nice addition since the Agency Review Draft, but we are confused by one of the targets included in it: “Microcystis aeruginosa cell density < 50% of the blue-green algae biomass, or < 20,000 cells/L (which ever is lower)” (p 5-2). We agree that the Microcystis aeruginosa cell density < 20,000 cells/L is an excellent target, but the Microcystis aeruginosa cell density <50% of the blue-green algae biomass it is unnecessary and not supported. For example, if the total blue-green algae biomass is very low, then it should not matter if Microcystis aeruginosa is 50% of the total -- because the total amount of Microcystis aeruginosa would still be very low. Public health risks are driven by the concentration of Microcystis aeruginosa cells and microcystin toxin, not the relative percent of the blue-green algae biomass that is Microcystis aeruginosa. We suggest a revised target of simply “Microcystis aeruginosa cell density < 20,000 cells/L”. This is the only place in the entire TMDL that we can find any mention of a 50% target, so we suspect that its inclusion in Table 5.1 may have been unintended. All other targets listed in Table 5.1 are justified and we support them. ___________________________________________________________________________________________ QUARTZ VALLEY INDIAN RESERVATION - COMMENTS ON PUBLIC REVIEW DRAFT, STAFF REPORT, KLAMATH RIVER TMDL AND ACTION PLAN, AUGUST 2009

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Klamath Hydroelectric Project (sections 5.3.2 and 5.2.3) The Public Draft TMDL now includes an additional allocation (required load reduction) to the Klamath Hydroelectric Project reservoirs in California (Iron Gate and Copco Reservoirs) that was not part of the Agency Review Draft. The quiescent waters of the reservoirs facilitate blue-green algal blooms, causing predictable exceedances of chlorophyll and Microcystis/microcystin targets even when assuming estimated natural background nutrient concentrations for reservoir inflows. In contrast, there are no predicted violations of the chlorophyll and Microcystis/microcystin targets with estimated natural background nutrient concentrations with the reservoirs absent. Thus, the Public Draft TMDL now includes an allocation requiring PacifiCorp to reduce upstream nutrient loads to an amount that will not cause predicted exceedances of chlorophyll and Microcystis/microcystin targets. We agree it is reasonable to require PacifiCorp to reduce nutrients to compensate for the fact that the physical characteristics of the reservoirs create the conditions favorable for blue-green algal blooms. The required reductions are equivalent to 10% of current conditions for total phosphorus and 12% for total nitrogen (Table 1). Table 1. Comparisons of annual total nitrogen and total phosphorus loads at Stateline under various scenarios, compared with the reductions required from PacifiCorp. Percentages are calculated based on information presented in the TMDL.

PacifiCorp Allocation (Required Reduction)

Nutrient

Existing Condition

(lbs)

Natural Baseline

Condition (lbs)

Oregon TMDL

Compliance (lbs) (Lbs)

(% Existing

Condition)

(% Natural Baseline

Condition)

(% Oregon TMDL

Compliance) Phosphorus 722,659 105,538 113,210 74,569 10% 71% 66%

Nitrogen 3,040,279 1,128,968 1,471,629 379,975 12% 34% 26% We present the reductions in this form to provide some context. While these reductions are substantial relative to natural conditions, they are small (10 to 12%) relative to current conditions. It is important to understand that if PacifiCorp were able to successfully implement upstream actions to reduce nutrient loads by the required amount, but if other major efforts to reduce nutrient loads were not also successful, then PacifiCorp’s reductions alone would not be sufficient to prevent blue-green algal blooms in the reservoirs. Thus, an argument could be made that PacifiCorp’s allocation is not sufficiently restrictive and that if PacifiCorp wants to keep its reservoirs in place, then the TMDL should require PacifiCorp to reduce nutrients down to levels where blue-green algal blooms would not occur in its reservoirs -- regardless of the actions of other upstream entities. This is probably a moot point, however, because, in our opinion, there is no way for PacifiCorp to meet its temperature allocations other than through dam removal. Thus, the magnitude of PacifiCorp’s required nutrient reductions is only of minor importance, and the amount currently proposed in the TMDL would appear reasonable. The “compliance lens” for D.O. and temperature within the reservoirs water column is of concern for meeting beneficial uses of the cold-water fishery. This is essentially a


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thermal and oxygen refuge for salmonid passage to the upper basin. Thermal refuges are providing critical habitat today, and found to be used historically in the TMDL temperature and oxygen analysis. However, cumulative effects to the salmonid resource have exacerbated the need for thermal refuges. One example is the thermal refuge usage on the Scott River, tributary to the Klamath, where tributaries are not accessible due to cumulative effects disconnecting access from the mainstem Scott. Thermal refuges are often unnaturally high in density, surrounded by warm water, both being stressful on fish which can lead to the increased spread of certain diseases (ich, columnaris). Fish isolated in refuge pockets are also more easily predated on. It should also be expected that the compliance lens would expand and contract over a 24-hour period as do refuges in the basin, this poses complications for compliance monitoring in such large reservoirs. The only way to ensure safe passage through the reservoir is to meet the water quality objectives of the Basin Plan throughout the reservoirs.

Other important allocations and targets for the reservoirs remain the same as they were in the Agency Review Draft, and we support them: - No reservoir-caused temperature increases allowed - Zero nutrient loading from reservoir bottom sediments Chapter 6: Implementation Plan General comments on Chapter 6 Many aspects of the implementation plan look good on paper, such as its requirements for farmers to develop water quality management plans, yet it remains to be seen how effective these efforts will actually be in practice. Overall, the implementation plan should be stronger and, while maintaining reasonable flexibility for those engaged in good-faith efforts to comply, the plan should be more explicit about how it will prevent unwarranted delay on the part of non-compliers. Timely implementation will be critical to the success of the TMDL. Many of the drivers of water problems (e.g. Shasta and Scott River flow depletion, the Klamath Hydroelectric Project, and Upper Klamath Basin agricultural pollution) were identified decades ago, yet positive action has been too slow taking place. We strongly encourage the Regional Water Board to fast-track implementation of solutions to these key problems to the absolute extent possible. 6.1.1 Basin-Wide TMDL Implementation This section of the Public Draft TMDL correctly identifies the main actions required to restore the water quality of the Klamath River: - Reduction of point and nonpoint source nutrient loads in Oregon and California; - Protection of thermal refugia; and - Addressing water quality impacts from the Klamath Hydroelectric Project. 6.1.3 Nonpoint Source Land Use Activities and Controls Tables 6.1 and 6.2 provide a useful summary of the regulatory mechanisms proposed for dealing with nonpoint sources of pollution. One suggestion for improvement would be to speed up the timeline for the waiver/WDRs for irrigated agriculture from 2012 to an


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earlier date. Irrigated agriculture is one of the largest contributors to nutrient-related Klamath River water quality problems. The sooner implementation begins the better. 6.2 Implementation of Allocations and Targets – Stateline Reducing nutrient inputs from the Upper Klamath Basin is a key issue in successful implementation of the Klamath River TMDL. The challenge is daunting given the weak laws governing water quality protection in Oregon. We encourage the Regional Board to exert strong pressure on upstream dischargers and regulatory agencies, to increase the chances of the program’s success. 6.4 Implementation of Allocations and Targets - Tributaries and Coordination with Existing Klamath River Tributary TMDLs 6.4.3 Lost River We support the concept of the development of a Management Agency Agreement (MAA) between the Regional Board, U.S. Bureau of Reclamation, and the U.S. Fish and Wildlife Service. We question, however, the necessity for the MAA to include an action item to “Complete a water quality study to characterize the seasonal and annual nutrient and organic matter loading through the KIP and refuges.”(p. 6-21). The technical analyses conducted in the development of the Lost River TMDL have already provided this. If not, then what was the purpose of the Lost River TMDL? The only thing accomplished by conducting yet another study would be a delay in water quality restoration. What is needed, in fact, are detailed work plans for the types of project that would be most effective in cleaning up water quality pollution in the Lost River basin, the prioritization of projects, and implementation of the highest priority projects. As noted in previous comments by QVIC (2007) and Yurok Tribe (2009), the Lost River and Lower Klamath Lake ecosystems have been profoundly diminished and degraded over the past century. A major component of the water quality problems of these areas is not just nutrient pollution, but also channelization, diking, and simplification -- the loss of connection between stream channels and wetlands. This lack of habitat complexity reduces the ability of wetlands and riparian vegetation to serve as nutrient sinks. If TMDL implementation in the Lost River and Lower Klamath Lake is to succeed the continuing trend of habitat degradation and channel simplification must be reversed. Reductions in nutrient inputs, alone, will not be sufficient to restore ecosystem function. The Problem Statement in Chapter 2 contains some discussion on this topic (see Degraded Channel Habitat Integrity on page 2-35), but its discussion in the Implementation Plan in Chapter 6 is inadequate We encourage Regional Board staff to lay out a more bold restoration vision in the Implementation Plan, even if the Board lacks the clear authority to guarantee its outcomes.

The Klamath TMDL should call for a plan to restore water storage and water filtration capacity to Lower Klamath Lake as a means of decreasing nutrient loads to the Klamath River and improving water supply. Historically, Lower Klamath Lake not only stored substantial quantities of Klamath River water but also likely removed huge amounts of nutrients with its extensive marsh system. We recommend consideration of increasing the size of Lower Klamath Lake, since much of the former lake bed is in public ownership, and using it to store and remove nutrients from Lost River water that are currently being flushed into Keno Reservoir and the mainstem Klamath River. Shasta and Scott Rivers (sections 6.4.4 and 6.4.5) Flow problems in the Scott and Shasta Rivers will confound Klamath TMDL implementation success. Not only is the ecosystem function of these tributaries compromised, but substantial cold water volumes which historically contributed to the mainstem have been lost. In their place we now have hot, nutrient rich irrigation tailwater. U.S. Geologic Survey flow records for both basins for June through August (Figures 2 and 3) show that both are dropping below 10 cubic feet per second and well below their historic norms. These reduced flow levels are creating extremely poor water quality and a collapse of fish carrying capacity. Flow records indicate the Shasta is steadily going dry. The lack of action under the Shasta and Scott River TMDLs, despite their approval and adoption into the Basin Plan does not bode well for the future of Klamath TMDL implementation.

Figure 2. USGS flow data for the Scott River in summer 2009.


15

:lUSGSUSGS 11519500 SCOTT RNR FORT JONES CA

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l> Hedian daily statistic (67 years)- Discharwe

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Figure 3. USGS flow data for the Shasta River in summer 2009.

There needs to be immediate action by the SWRCB water rights division to ensure that adjudicated flow levels are met on the Scott and Shasta Rivers. The Department of Fish and Game appears to have lost any stomach for fish protection and enforcement in these two basins in its attempt to win support for its proposed Incidental Take Permit (ITP) for coho salmon for agricultural activities (ESA 2008a, 2008b) under the California Endangered Species Act (CESA). The National Marine Fisheries Service has failed to take action despite virtual dewatering of ESA-listed coho salmon habitat in both basins. Regarding the Scott River, the Draft TMDL notes that “Attainment of the Klamath River temperature TMDL, and associated temperature standards, requires that this study move forward and that appropriate management practices are implemented following the study in order to ensure adequate flow in the Scott River.” But there has been no effective action to restore Scott River flows. 6.5.1.1 Riparian Shade Allocations and Targets (Watershed-Wide) We support the protections for riparian vegetation proposed in this section. 6.5.2 Watershed-wide Prohibition on the Discharge of Excess Sediment We support the proposed watershed-wide prohibition on the discharge of excess sediment applying to all sediment sources in the Klamath River not regulated under a Regional Water Board adopted WDR or waiver. 6.5.3.1 Implementation Measures to Protect Thermal Refugia: Flow We strongly support the language in section 6.5.3.1 that Regional Water Board staff “will work with other state and federal agencies and tribes to identify and eliminate illegal diversions in the Klamath River basin in California” and “recommend that the State ___________________________________________________________________________________________ QUARTZ VALLEY INDIAN RESERVATION - COMMENTS ON PUBLIC REVIEW DRAFT, STAFF REPORT, KLAMATH RIVER TMDL AND ACTION PLAN, AUGUST 2009

16

:lUSGSUSGS 11517500 SHASTA RNR YREKA CA

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17

Water Board staff issuing water rights permits to divert surface water in the Klamath River basin in California consider the impact of increased diversions on tributaries that provide thermal refugia.” (p. 6-28) 6.5.3.1 Prohibition of Discharge in and Around Known Thermal Refugia in the Klamath River Basin We fully support the proposed protections for thermal refugia, including the prohibition of waste discharge (e.g. suction dredge mining) in the mainstem Klamath River and in the lower sections of tributaries whose lower reaches serve as refugia. The maps and lists of specific refugia locations are also helpful in making this proposal understandable. Only thermal refugia habitat on the mainstem Klamath is documented in the Appendices of the TMDL. USFS Klamath National Forest, QV tribe and Northern California Resource Center have been collecting thermal refugia data in the Scott since 2004. A comprehensive map of all identified locations in the lower 21 miles of the Scott is attached to be included for protection. Also to be noted and included for protection is a reach of approximately 5 miles that during the summer serves as a thermal refuge to salmonids in the mainstem Scott River. This has been documented in studies conducted by USFS, NCRC and QV tribe since 2004. Salmonid densities are significantly higher throughout this reach. The temperature drop over this stretch of the Scott River was first noted in the ’03 TIR and again in the ’06 TIR conducted by Water Sciences. The Klamath TMDL lists Boulder, Kelsey and Canyon Creeks as important refugia for salmonids; but in fact, the entire 5-mile stretch (Boulder Creek to Townsend Gulch) is critical habitat during the summer rearing bottleneck. I have attached the following reports describing the fish usage in this thermal refuge reach: Maurer 2006, 2007 and 2008. Clarification of the thermal refugia definition: Chapter 6-28 states, “Thermal refugia are typically identified as areas of cool water created by inflowing tributaries, springs, seeps or through upwelling hypoheric flow and groundwater in an otherwise warm stream channel.” Summer rearing studies in the Scott River indicate that not all cool-water inflows necessarily offer fish refuge due to site specific and ambient water quality conditions. The statement in the TMDL, Chapter 6 should read something like: “Thermal refugia are typically identified as areas of cool water created by inflowing tributaries, springs, seeps or through upwelling hypoheric flow and groundwater in an otherwise warm stream channel offering refuge habitat to cold-water fish/aquatic species.” It seems that the effects (settling distance) of sediment associated with suction dredging would be dependant on flow? Where does the ~300ft number come from? Moreover, at what flow does it settle out at 300ft? No citation is listed in the Klamath TMDL Implementation Plan as to how this number for protection was determined. Please provide some scientific support for this determination. Tributaries should have pollution protection to the upper most identified location of summer rearing and/or spawning anadromy, not just the lower 3000 ft. By protecting only the lower 3000 ft, you could unintentionally inflict overcrowding and increase competition if pollution is ‘allowed’ and occurs above 3,000 ft.


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6.5.4 Road Construction and Maintenance We support the actions proposed in this section to regulate construction and maintenance of private, county, and State roads. 6.5.5 Grazing We support the Public Draft TMDL’s requirement that: “...any party conducting grazing activities in the Klamath River basin must select and implement management practices that control sediment sources, protect and maintain riparian functions, and address discharges of nutrients and organic matter.” (p. 6-38), and that “To control discharges of nutrients and organic matter from animal waste deposited to surface waters, Regional Water Board staff recommend including, as a condition of eligibility for general WDRs or a waiver, that responsible parties implement measures to limit livestock access to the stream channel.” (p. 6-39). In combination with low flows, nutrient loading from cattle waste can promote eutrophication and elevate pHs that can be directly stressful to fish or that can promote the production of highly toxic dissolved ammonia. While we recognize that with proper management it is possible to allow cattle limited access to stream channels and not cause ecological harm, such protective practices are, however, difficult to achieve. Large sums of public money have been used to construct riparian fencing in the Klamath Basin yet there is little enforcement and monitoring to ensure that the fencing is maintained and effective, and that riparian vegetation is actually re-generating. It may prove more effective to simply mandate that cattle be completely excluded from stream channels, rather than to “limit” access. The proposal to require ranch management plans is good, and it contains common-sense provisions such as allowing landowners to cooperate on group plans, and to modify and adapt existing plans to fit TMDL requirements. Under sub-section 6.5.5.1 title: “Responsible parties” conducting grazing activities in Klamath Basin. It should state more clearly if a permit or lease is given to a rancher for grazing on another private landowners property exactly who is responsible for implementing the BMP’s, meeting water quality objectives and for compliance oversight. And what data will be made public. 6.5.6 Irrigated Agriculture We support the Public Draft TMDL’s proposal to require the development and implementation of water quality management plans to control sediment, nutrient, and temperature effects rising from irrigated agriculture. We also support the proposal for developing a Klamath River basin-wide conditional waiver of WDRs and/or general WDRs for irrigated agriculture. We request that any group compliance programs be transparent, have enforcement oversight, be open to stakeholder input during the drafting of the WDR and that results will be shared. The implementation plan should be strengthened by requiring on-farm treatment of all agricultural wastewater or tailwater throughout the Klamath Basin. The use of constructed wetland catchments would increase percolation to groundwater, reduce


19

adverse warm water impacts and strip nutrients that would otherwise reach streams. Wastewater can also be retained in small catchments and pumped as a source of nutrient rich water for reuse in irrigation, as has already been demonstrated on some Shasta River ranch lands. 6.5.7 Timber Harvest (on Private Lands) With regard to timber harvesting on private lands, the Klamath TMDL calls for the application of California Department of Forestry (CDF 2009) Threatened and Impaired watershed rules throughout the Klamath River Basin because of watershed-wide need for protection. We strongly support this recommendation. Another valid improvement for TMDL implementation is increased timber harvest restrictions in Class III water courses, intermittent headwater streams, to prevent alteration to channel structure. This is needed since these areas are often steep and unstable. 6.6 TMDL Implementation on Federally Managed Lands, Timber Harvest, Grazing The Klamath TMDL clearly defines the need to protect cold water refugia. The zero increase in sediment target for Middle Klamath tributaries will help achieve that objective. However, there are no targets or thresholds to limit disturbance and risk of cumulative effects that have been a pervasive problems in the basin (Kier Associates 1999). Recent information provided by USFS Region 5 hydrologist Barry Hill (2009) indicates that the cumulative effects risk has actually increased on the Klamath National Forest and that there are now 50 watersheds recognized as over cumulative effects thresholds:

“The Klamath National Forest had 45 watersheds above TOC in 2004, based on three separate models. Since 2004, two watersheds on the Klamath NF have gone over the TOC threshold due to timber harvests and 13 have gone over threshold due to wildfires. During the same period, six watersheds that were above TOC fell below threshold due to passive recovery and four watersheds fell below threshold due to road treatments. The current total of watersheds over TOC is therefore 50.”

The Klamath TMDL proposes the use of waste discharge requirement (WDR) permits or negotiated waivers as a means to prevent non-point source pollution and protection of refugia. This strategy is logical and could be successful, but we are concerned about recent efforts by SWRCB staff (2009) to shift management authority for USFS oversight to Sacramento and to eliminate Regional Water Board participation. Past comments by Work Group members on the Klamath and Scott River TMDLs have clearly established problems with regard to Klamath National Forest sediment pollution and the need for improvement in land management to be more compatible with Pacific salmon protection and restoration and Clean Water Act compliance. It is absolutely necessary that the Regional Water Board continue in its on-the-ground oversight role and that the Memorandum of Agreement (MOA) that governs timber harvest and grazing be completed in a timely manner since it is a critical link in


20

successful TMDL implementation. As mentioned in previous comments, the MOA should also increase the monitoring requirements of USFS staff and the timely provision of data for trend monitoring for adaptive management. Comments from the Quartz Valley Indian Reservation (2009) to the SWRCB regarding the proposed changes in USFS oversight in the Klamath Basin are included here as appendix 1 to these comments and are submitted here for the Klamath TMDL record. The goal of protecting tributary refugia will be confounded by increased peak flows caused by timber harvest and road building in the rain-on-snow zone (3,500-5,000 ft elevation), which the TMDL continues to ignore. Rain on snow events can increase peak discharged that widen stream channels and make streams more subject to warming. Van Kirk and Naman (2007) point out that the snow elevation is rising due to climate change and this means that rain-on-snow effects can extend to still higher elevations and increase the risk of damage. KNF has many watersheds with high-elevation headwaters and potentially increased peak flow risk. Firm targets for limiting road densities, and dates for their attainment are needed to prevent still more flood damage to refugia. Another issue is the inability to keep grazing allotments in close proximity from merging with one another. An increased number of cattle on one allotment leads to over-grazing and the increase of nutrients and pathogens. USFS allotments in the Scott border private timber grazing allotments and this merging of cattle onto the high mountain lake allotment creates pollution beyond the assimilative capacity of the lake/inlets/outlets, data collected from the Shackleford Creek allotment (Campbell Lake) by the QV Tribe in 2007 found high levels of E.coli. 6.7 Klamath River Water Quality Accounting and Tracking Program (KlamTrack). We are very supportive of the general concept of KlamTrack, but there are important details that are not yet addressed and need further development. There must be strong evidence and a high likelihood that any pollution trading allowed will have at least as positive an effect on water quality, at the site of the discharge, as pollution control done in a “normal” way – that is, pollution reduced at the source, rather than at an alternate site. Given that pollution trading could result in substantial economic benefit to the entities responsible for pollution discharges, because pollution trading could be much cheaper than on-site compliance, the burden of proof should be on such entities to demonstrate that pollution trading would be effective. Also, due to the uncertainties surrounding effectiveness the predicted outcomes of pollution trading should contain some safety factor (i.e. >200% of the effectiveness of on-site compliance, perhaps larger if the uncertainties were very large) to assure that goals are met. One shortcoming of the proposed KlamTrack Program is the lack of specific mention of Tribes in the development of the program. This should be rectified.


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Chapter 7: Monitoring Program General comments on Chapter 7 The monitoring plans within the Draft TMDL reflect years of work and a great deal of collaboration with scientists from other agencies, Tribes and private entities and it sets new standards for thoroughness for a TMDL. The strategy laid out is logical, methods are scientifically valid, and maps and tables are clear and powerful summaries. Additional monitoring, however, is recommended at some locations because there are large geographic areas where there is insufficient coverage to gage results of TMDL implementation (i.e. Middle Klamath). The special studies section shows that Regional Water Board staff understand where there are critical knowledge gaps and they are to be commended for taking an interdisciplinary approach to understanding Klamath River water quality and fish health problems. There are many locations in the basin where there are accepted assignments for monitoring responsibilities by tribes, agencies, Resource Conservation Districts (RCDs), PacifiCorp and other private parties, but given past experience we have concerns that not all these data will in fact be made available. The final Klamath TMDL needs to go further and state that monitoring data collection and sharing will be mandatory under Waste Discharge Requirement (WDR) permits, Waivers of WDRs and in the Memorandum of Agreement (MOA) envisioned with federal agencies. The map of locations for monitoring (Figure 4) reflect a major strategic effort and results from these locations will go a long way towards understanding water quality trends and in helping gauge TMDL implementation success. The rationale for location and parameters measured is clearly defined in Table 7.3 and the summary in this form is very useful. Similarly Table 7.7 displays a matrix of parameters and locations as showing the periodicity of sampling, which is an important element of understanding temporal patterns of Klamath River water pollution. Our comments below provide some suggestions for improving the monitoring plan. Comments regarding data sharing We recommend that requirements for monitoring and data sharing be made explicit. The Regional Water Board has the authority to require monitoring and data sharing as part of all WDRs, Waivers and MOAs, and we strongly encourage that the Board utilize that authority. The Draft TMDL relies in part on a spirit of cooperation through the KBWQMCG, but experience shows that both private parties and organizations like KNF sometimes withhold data that discloses conditions that do not reflect well on management. It is unrealistic to rely on entities to release data that is contrary to their self-interest. For example, KNF collected extensive data from lower Scott River and Middle Klamath tributaries after the January 1997 storm that are not available in raw form. Related studies were never completed or produced for public dissemination that gave more in depth information about damage to channels, although de la Fuente and Elder (1998) reported 437 miles of channel scour on KNF from that event. For years, PacifiCorp failed to tell the public or regulators about its finding that toxic algae were commonly present in Copco and Iron Gate reservoirs, until the Tribal sampling also discovered the algae brought the issue to public’s attention. Lack of data sharing by the Siskiyou RCD


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discussed above is another example. These examples all point to the need for the Regional Board to make data provision a requirement of all permits. The Draft TMDL describes new efforts to set up a data sharing mechanism “allowing users to contribute, access and download data” in order to “encourage the transfer and sharing of fundamental water quantity and quality information amongst monitoring organizations needed to inform water resources studies.” It envisions a “web portal” hosted by a third party for accessing and uploading data. While such a tool would obviously be helpful in facilitating data sharing, it will not guarantee that all entities will upload their data. 7.1.1 Components of the TMDL Monitoring Program In this section, the Draft TMDL touches in implementation monitoring and the need for documentation that “can be as simple as a photographic record of activities.” (p. 7-2). We recommend that the final Klamath TMDL should require photo monitoring points as a condition of all permits. There should be a minimum five year history of photo documentation with reports or annotation to see trends at the site and whether the project succeeded. Language should include the need to take pictures after large storm events or wet high flow years. 7.4 Public Health Monitoring Cyanotoxin monitoring and issuance of public health warnings is an appropriate step given the significance of this pollution issue in Klamath Hydroelectric Power reservoirs and in the lower Klamath River below Iron Gate Dam. The inclusion of tissue sampling of Klamath River freshwater mussels and fish is also appropriate. Findings of potentially hazardous levels of cyanotoxin on yellow perch in Copco Reservoir should prompt health advisories from the County of Siskiyou to protect its citizens. 7.5 TMDL Ambient Compliance and Trend Monitoring This section is too mainstem-centric, and should be expanded to include more monitoring of tributaries. While Chapter 5 of the TMDL includes targets and allocations regarding tributary shade and sediment, the monitoring plan does not proposes any monitoring to track progress towards reaching the targets and allocations. The Draft TMDL states that “the sampling frequency and density should be of a high enough resolution and over a reasonable period time to determine whether management actions are having the desired effect on water quality conditions.” (p. 7-2). The map of locations where the Regional Water Board has a commitment for monitoring (Figure 4) shows a large number on Six Rivers National Forest (SRNF) in the lower Middle Klamath Basin, but almost none on Klamath National Forest (KNF) further upstream. Most of the data SRNF is supplying are likely from automated temperature probes and there is no reason that KNF should not be supplying similar data for Middle Klamath (e.g. Elk, Grider) and also for lower Scott River (e.g. Kelsey, Canyon) tributaries that serve as Pacific salmon refugia. Figure 5 shows water temperature data previously collected for the Middle Klamath (MKWC 2008) and all of these stations need to be added. If the USFS cannot provide staff to collect, process and submit data, then they should be required to provide funding for other entities such as the Salmon River

Restoration Council (SRRC), Quartz Valley Tribe, Karuk Tribe or the Middle Klamath Watershed Council (MKWC) to do so.

Figure 4. This map shows a detailed area taken from Figure 7.1 in the Draft TMDL and shows lack of sufficient stations in the Middle Klamath and Scott River basins.


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Figure 5. This chart shows floating weekly average water temperatures at the mouths of Middle Klamath tributary tributaries and in the mainstem Klamath River. All tributaries should have automated temperature probes every year. From MKWC (2006). The USFS must also be compelled through the MOA to supply all other trend data, such as V*, bulk gravel samples, habitat surveys, macroinvertebrate data and other standard metrics so that patterns of degradation and recovery trajectories can be developed. Such data can be used to assess aquatic habitat quality (Kier Associates and NMFS 2008). Macroinvertebrate data are increasingly powerful for water quality analysis because of regional studies that allow understanding of communities associated with intact aquatic habitats and those associated with different levels of impairment (Rehn et al. 2007). The basin-wide monitoring location map (Figure 4) also shows a significant problem with lack of provision of monitoring data in the Scott River. While the Shasta Valley RCD has apparently committed to supplying data in the Shasta basin, the Siskiyou RCD appears to be making no similar commitment. There are over two dozen water temperature monitoring locations that have been monitored routinely in the Scott Valley and trend data for these locations is essential for understanding compliance with permits and gauging trends resulting from TMDL implementation. The health and water quality of the mainstem Klamath River is tied to that of major tributaries like the Scott River and to have significant data gaps is therefore troubling. We recognize the resources available for monitoring are always limited, but we are disappointed to see the recommended frequency for most nutrient sampling locations is monthly. For the purposes of constructing mass-balances, biweekly (every two weeks) would be far better. One compromise between monthly and bi-weekly sampling would be to have monthly sampling at most stations, but then biweekly sampling at a subset of stations such the mainstem Klamath USGS gages: Iron Gate, Seiad, Orleans, and Turwar. ___________________________________________________________________________________________ QUARTZ VALLEY INDIAN RESERVATION - COMMENTS ON PUBLIC REVIEW DRAFT, STAFF REPORT, KLAMATH RIVER TMDL AND ACTION PLAN, AUGUST 2009

24

Middle Klamath Tributary and Malnstem Klamath River Temperatures 2006

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7.6 Additional Monitoring Needs and Key Questions for Special Study Consideration The Draft TMDL goes beyond requirements of just assessing pollution loads and setting limits, it tries to help focus additional research and monitoring on answering key questions about linkages between river dynamics, flows, water quality and fish health. Sections on the relationship of fish disease and water quality conditions in the Draft TMDL are excellent and appropriate studies are recommended. The Regional Water Board might consider specifically mention the need to explore algal bed dynamics, water quality fluctuations and non-normative water pollution events (Higgins 2009). The Draft TMDL cites the need to assess nutrient mass balance to “better understand the sources and sinks of nutrients and organic matter, in the Klamath River basin.” (p. 7-2). We recommend that the TMDL specifically recommend a study of the nutrient removal capacity of a re-expanded Lower Klamath Lake, and also estimate the increase in summer water availability from storage excess of Lost River flow. During high-flow months/events, the current water management practice is to route water from the Lost River into the Klamath River through the Lost River Diversion canal. It may be feasible to route that water instead into Lower Klamath Lake, then release it back into the Klamath River during lower-flow months. The Comprehensive Water Quality Monitoring special study includes a recommendation to collect water samples at the springs below J.C. Boyle Dam. We agree that this is a critical data gap, given the large volume of flow contributed by these springs and the uncertainty regarding their nutrient concentrations. It is our understanding that sampling these springs is logistically difficult, even potentially dangerous, because it requires kayaking or skilled rock-hopping to reach the site, then diving down to the bottom of a pool in swift water to collect the sample (the springs do not cascade in from the bank, they enter from the bottom of the river bed). We strongly encourage someone to do the sampling, even as a stand-alone exercise not part of the Comprehensive Water Quality Monitoring special study. We support the proposed Periphyton Characterization in the Mainstem Klamath River special study, but think that the number of samples should be expanded to include at least one sample in July, August, and September. One of the key uncertainties in Klamath River water quality is relative importance of the factors that govern growth and decay of periphyton, and the resultant effects on pH and dissolved oxygen. For example, how will the periphyton react to changes in nutrient concentrations and water clarity based on upstream management changes and/or dam removal? What are the triggers for summer proliferation and fall senescence (e.g. day length, flow, temperature)? The Klamath TMDL model provides an answer to some of these questions; however, it may not be the correct answer, given that it does not include key factors influencing periphyton such scour. For example, the Klamath TMDL model predicts that mainstem Klamath River periphyton biomass peaks in late June or early July, whereas field data indicate that biomass is just starting to proliferate during that time and does reach a peak until late August or September.


26

The final Klamath TMDL should include a special study recommendation to discern the length of time required for recovery of stream channels from cumulative effects from events such as the January 1997 storm. Channel scour events flatten stream profiles, diminish pool frequency and depth, alter riparian conditions dramatically and substantially elevate water temperatures. Elk Creek is one case study referenced by de la Fuente and Elder (1998) as having experienced substantial increase in water temperature; data are needed to understand how long it takes this major refugia to recover. Studies on the Elk River in Oregon by the USFS (1998) showed how water temperature recovered after logging and flood damage, and we recommend that Regional Water Board staff require a similar analysis from the USFS as part of the MOA currently in development. The study might be best conducted or overseen by the USFS Pacific Southwest Forest and Range Experiment Station (Redwood Sciences Lab) with collaboration including Regional Water Board staff and KNF resource scientists. Tools such as the shallow landslide stability model (Dietrich et al. 1998) should be recommended to discern associations of land management on steep ground and sediment yield (Kier Associates 2005). In this way past mistakes can be avoided and disturbed areas in high SHALSTAB risk zones could be prioritized for treatment. The mouths of streams that serve as refugia should also be studied using aerial photos from different eras to determine changes in channel width as an index of recovery (Grant 1988). Similar studies should also be conducted on mixed ownership basins like Beaver and Horse Creek, which are critical refugia and have a checkerboard land ownership pattern of private timberlands and USFS holdings. Co-participation of private timber companies should be a requirement of WDR or Waivers under TMDL implementation and complete data transparency needs to be required of private parties as well. Other comments on Chapter 7 Also, there appears to be some errors in Table 7.7: - The site “Klamath River at Shasta River at Walker Bridge (RM- 176.7)” is listed, when in fact this actually is two separate sites: Klamath River above Shasta River (river mile 176.08) and Klamath River at Walker Bridge (river mile 156.00). - Klamath River at Brown Bear River Access is not river mile 157.5, it is 150.0 (see http://mapper.acme.com/?ll=41.82314,-122.96104 and http://www.fs.fed.us/r5/klamath/recreation/rivercenter/rivermaps/map3.shtml) We are disappointed to see the TMDL proposing a new 6-digit site ID system (i.e. Klamath River at Seiad Valley is “KR1285”) when there is already an existing 7-digit site ID system in use. Much of the nutrient and automated probe water quality data collected in the Klamath River and its tributaries collected up through 2005 has been compiled into a single Microsoft Access database. The database was begun by PacifiCorp (2004) and added to through other studies, such as the development of Klamath TMDL, nutrient budgets for Iron Gate and Copco Reservoirs (Kann and Asarian 2005), and nitrogen budgets for river reaches below Iron Gate Dam (Asarian and Kann 2006). That database, including lookup tables of site IDs, is available online at: http://www.krisweb.com/ftp/KlamWQdatabase\KR_TMDL_database_with_PCorp_USFWS_CDWR_data.zip

http://mapper.acme.com/?ll=41.82314,-122.96104

http://www.fs.fed.us/r5/klamath/recreation/rivercenter/rivermaps/map3.shtml

http://www.krisweb.com/ftp/KlamWQdatabase/KR_TMDL_database_with_PCorp_USFWS_CDWR_data.zip

http://www.krisweb.com/ftp/KlamWQdatabase/KR_TMDL_database_with_PCorp_USFWS_CDWR_data.zip


27

PacifiCorp has continued (mostly, but with a few exceptions) to use the same Site ID system in their 2006-2008 reports. Figure 4 and Table 2 show a sub-selection of sites and their 7-digit site ID codes. The TMDL states that the “station ID’s are per the KBWQMCG.”, but we do not see any mention of them in KBWQMCG documents such as Royer and Stubblefield (2009). It would be a waste of time to re-invent the wheel unless it is absolutely necessary.

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Figure 6. Location of nutrient sampling sites in the Klamath River and its tributaries. Note that the Site ID code for mainstem stations begins with “KR”, followed by 5-digit river mile (i.e. KR18973 is river mile 189.73). Figure from Asarian and Kann (2006).


28


29

Table 2. Key and description for nutrient sampling locations shown in Fig. 2. Note that the Site ID code for mainstem stations begins with “KR”, followed by 5-digit river mile (i.e. KR18973 is river mile 189.73). Table from from Asarian and Kann (2006).

Site ID River Mile Site Name Latitude Longitude

KR00010 0.10 Klamath River Estuary Mainstem 41.543610 -

124.078890

KR00579 5.79 Klamath River at Klamath Glen 41.515280 -

123.998890

KR02400 24.00 Klamath River at Johnson's Point 41.347630 -

123.876000

KR03720 37.20 Klamath River at Young's Bar 41.246600 -

123.773300

KR03850 38.50 Klamath River above Tully Creek 41.228060 -

123.772220

KR04033 40.33 Klamath River at Martins Ferry 41.207220 -

123.755280

KR04350 43.50 Klamath River at Weitchpec 41.185830 -

123.703056

KR05912 59.12 Klamath River at Orleans 41.303330 -

123.533330

KR10066 100.66 Klamath River below Happy Camp 41.729720 -

123.424440

KR12858 128.58 Klamath River at Seiad Valley 41.854170 -

123.230280

KR13085 130.85 Klamath River at Seiad Valley (2.25 mi above gage) 41.837333 -

123.197500

KR14261 142.61 Klamath River above Scott River 41.781530 -

123.033110

KR14903 149.03 Klamath River below Everill Creek 41.808133 -

123.014067

KR15850 158.50 Klamath River at Round Bar Pool 41.851000 -

122.835530

KR16075 160.75 Klamath River d/s Beaver Creek 41.865800 -

122.819300

KR16079 160.79 Klamath River at Gottsville River Access 41.858450 -

122.750220

KR17608 176.08 Klamath River above Shasta River 41.831280 -

122.593467

KR18238 182.38 Klamath River u/s Cottonwood Creek 41.892730 -

122.535400

KR18952 189.52 Klamath River below Iron Gate Dam (USGS Gage) 41.928056 -

122.443056

KR18973 189.73 Klamath River below Iron Gate Dam (Hatchery Br.) 41.931600 -

122.440000

KR19645 196.45 Copco Dam Outflow 41.973250 -

122.363580

KR20642 206.42 Klamath River u/s Shovel Creek 41.972100 -

122.201600

KR21970 219.70 Klamath River below Boyle powerhouse at USGS gage 42.083112

-122.071746

KR22040 220.40 Klamath River at J.C. Boyle Powerhouse 42.093060 -

122.070830

KR22050 220.50 Klamath River above J.C. Boyle Powerhouse 42.093610 -

122.069170


30

KR22460 224.60 Klamath River below J.C. Boyle Reservoir 42.121700 -

122.049400

KR22822 228.22 Klamath River above J.C. Boyle Reservoir 42.149900 -

122.015400

KR23334 233.34 Klamath River below Keno Dam 42.135300 -

121.947220

KR25312 253.12 Link River at Mouth 42.218900 -

121.788300

KR25479 254.79 Upper Klamath Lake at Fremont St Bridge 42.238300 -

121.788060

SA - Salmon River at Somes Bar 41.376900 -

123.477200

SCM - Scott River at Mouth 41.765830 -

123.022800

SCUS - Scott River at USGS Gage 41.640500 -

123.014500

SH00 - Shasta River at Mouth 41.825000 -

122.595100

SHUS - Shasta River at USGS Gage 41.823167 -

122.595000

TR - Trinity River at Weitchpec 41.184330 -

123.704167

TRHO - Trinity River at Hoopa 41.050400 -

123.673300


31

Appendix 1: Proposed Site-Specific Dissolved Oxygen Objective for the Klamath River in California Based on the results of the Klamath TMDL, Regional Water Board staff are recommending a change to Basin Plan dissolved oxygen (D.O) standards for the Klamath River. Staff’s justification for the proposed change is described in the Public Draft TMDL Appendix 1. In our comments here regarding Appendix 1, we discuss existing standards, the proposed revisions to the standard, and the strength of the justification for the change. Current Basin Plan (NCRWQCB 2007) D.O. standards are an absolute minimum of 7 mg/l for the Klamath River above Iron Gate Dam in California, including reservoirs and 8 mg/l below the dam (Table 3). The Basin Plan also currently sets a 50% limit, which is based on a calculation of the monthly means over the course of 12 months, of 10 mg/l above and below Iron Gate Dam. The Hoopa Tribe (2008) adopted values originally recommended by the NCRWQCB (2005), and these standards have been approved by U.S. EPA:

“Site-specific dissolved oxygen water quality objectives for the Klamath River are derived by calculating the daily minimum dissolved oxygen necessary to maintain 85% saturation under site salinity, site atmospheric pressure, and natural receiving water temperatures. In no event may controllable factors reduce the daily minimum DO below 6.0 mg/L.”

The Hoopa Tribe (2008) D.O. criteria are set for floating weekly average minima (7 DA Min) based on recommendations of U.S. EPA (1986) to reflect potential accumulated effects of recurring D.O. depression that can stress salmonids. The Hoopa standards also reflect the varying life history requirements of Pacific salmon species similar to those of Washington State (WDOE 2002) with a 7 DA Min of 8 mg/l year around (COLD) and 11 mg/l in the water column during spawning season (SPAWN). The latter reflects an estimated drop of 3 mg/l between surface water D.O. and that inside the redd pocket in the gravel (U.S. EPA 1986). Table 3. Comparison of current and proposed NCRWQCB D.O. standards and those of the Hoopa

ribe. Spawning period is September 15 to April 15. T Standard Minimum Minimum

SPAWN % Sat**

NCRWQCB Existing above Iron Gate 7 mg/l ----- ----- NCRWQCB Existing below Iron Gate 8 mg/l ----- ----- NCRWQCB Proposed 6 mg/l ----- 85% Hoopa Tribe 8 mg/l* 11 mg/l* 90% *7-day moving average (7 DA Min) ** Percent dissolved oxygen saturation at natural temperatures


32

The arguments to support this change in standards are offered in Appendix 1 of the Klamath TMDL: - Baseline data used to formulate existing Basin Plan standards (Table 3.1) were

collected in the 1950s and 1960s when conditions were already degraded and only diurnal samples were taken and standards should not be applied to continuous probe data that include nocturnal samples.

- Previous DO objectives for the Klamath River are consequently unachievable using modern monitoring equipment.

- Modeling of “natural conditions” indicates that the Basin Plan standard of 8.0 mg/l could not be met on the Klamath River between June and September even before anthropogenic disturbance.

- According to staff calculations, 85% saturation reflects minimum values resulting from variation in saturation that could occur within a healthy, free-flowing river as a result of normal photosynthetic activity and decomposition.

The Klamath TMDL concludes that life cycle based criteria, such as those adopted by the Hoopa Tribe (2008) are not achievable due to naturally high nutrient background conditions. As a practical matter, the Regional Water Board is currently confronted with routine violations of its current D.O. standards that make enforcement impractical, if not impossible. However, Regional Water Board arguments that historical conditions in the Klamath River would have fostered substantial annual or diel periodicity of D.O. swings are not well founded:

“The Klamath River begins in the upper basin as a low gradient river in nutrient rich volcanic soils where elevated loads of nutrients and organic material are released to the water column and flow downstream. This fuels elevated algal growth throughout the upper basin with a concomitant diel fluctuation.” (p. 13)

In fact, volcanic terrain drainage often results in water percolating into underground aquifers and arising as very high quality water, such as in the case of the Williamson River above Upper Klamath Lake. While phosphorous from volcanic terrain would have enriched aquatic ecosystem productivity somewhat, much of it would have been trapped before delivery to the water column by hundreds of thousands of acres of wetlands, marshes and riparian zones that surrounded lakes and streams before disturbance. Further, extensive marshes and wetlands surrounding Upper and Lower Klamath Lakes created slightly acidic conditions that limited some forms of blue-green algae, such as Aphanizomenon flos-aquae. The latter was not present 100 years ago and only became well established after extensive destruction of the marshes following World War II. It now produces enormous quantities of nitrogen. When the Klamath River was nitrogen-limited and marsh buffer and filter capacity was still intact, mainstem conditions may not have had the excessive nutrients to cause periphyton blooms and associated D.O. variability.

Further, water temperature conditions before mining, deforestation, dam construction and massive sedimentation were likely moderated by mainstem Klamath River hyporheic function (U.S. EPA 2003, ODEQ 2008). Thus D.O. would have been higher because water temperatures were likely historically lower before watershed disturbance. Due to complexities and uncertainties, hyporheic cooling is not included in the Klamath TMDL models, and thus is not reflected in model outputs for the natural condition scenario. Certainly, standards that cannot be met are not practical, but ascribing current impairment in conditions partially natural may be in error and does not foster a sense of urgency in what is a critical problem with D.O. in some reaches of the mainstem Klamath River. While one of the largest concentrations of spawning chinook salmon in the Klamath River occurs immediately below Iron Gate Reservoir, D.O. problems are pervasive during the spawning season (after September 15) on the mainstem below Iron Gate Dam (Figure 7). Data from the Karuk Tribe Department of Natural Resources (Karuk DNR 2008) show that the daily average surface water D.O. in October commonly drops below 7 mg/l. Data are lacking on streambed permeability below Iron Gate Dam. But,if there is a drop of 3 mg/l as estimated by U.S. EPA (1986),it would mean that in-redd D.O. was ranging from 3-5 mg/l. WDOE (2002) state that “average intragravel oxygen concentrations of 6-6.5 mg/L and lower can cause significant stress and mortality in developing embryos and alevin.” Although decreasing water temperature in the fall is a mitigating factor, that, too, is affected in the river below the dam due to the thermal mass of Iron Gate Reservoir. The result is likely very poor survival to emergence and acute selective pressure on fall

hinook below Iron Gate Dam. C


33

Figure 7. Floating daily average D.O. of the Klamath River below Iron Gate Dam for 2006-2008 show that depressions are occurring during Chinook salmon spawning season. Data from Karuk DNR (2008).

Klamath River below Iron Gate - DailyAverage Dissolved Oxygen, 2006, 2007, and

2008

Spawning

10/4 11/39/4S/5

-OS'IG 00 -OTIG DO I-OS'IG DO ---+.

7/S

10 ,------------------------,~

"00 9E~ SgecS 7..,~ 6

~ 5c4-1---~---~---~--~---___r_'

6/6

Date


34

To its credit, the Klamath TMDL recognizes the problems created by Iron Gate Reservoir and calls for consideration of dam removal as a means to remediate water pollution problems as well as for the protection of refugia. We have concerns, however, that the proposed D.O. standards may regard tailwater flows below Iron Gate dam as being in compliance with the TMDL and Basin Plan when in fact they reflect acute impairment. To help us assess whether we should support the proposed revisions to the D.O. criteria, we would like to see what the 85% saturation dissolved oxygen concentrations are under the TMDL’s natural conditions scenario for various locations along the Klamath River, including Iron Gate Dam. Discussions of setting criteria are necessary, but non-normative water quality events in the mainstem Klamath River (Higgins 2009) may be a greater concern with regard to fish health and source of juvenile salmonid mortality. For example, immediately after flows had been ramped down 1,000 cfs in late June and early July of 2008, USFWS (2008) dive crews found that most of the tagged Iron Gate Hatchery juvenile Chinook salmon they were tracking had not survived:

“The crew observed about 10 to 40 dead fish within 5 meters upstream and downstream of the location of each tag. Dead fish were observed at 23 of the 25 dives made. The appearance of dead fish observations ranged from what was assumed to be recent mortalities to carcasses fully engulfed by fungus. The two dives where dead fish were not observed occurred in water having relatively high water velocity. Dead and/or dying fish were also observed at several thermal refugia areas, which were also occupied by live salmonids (predominantly Chinook salmon, and to a lesser extent, steelhead). Most mortalities observed were juvenile salmonids; however, numerous dead sculpins, suckers, and one dead bullhead catfish were also observed.”

Higgins (2009) noted that water quality stress must have been acute to cause mortality of warm water fish species like suckers and explored potential relationships of flow changes, algae bed dynamics and non-normative water quality as a potential triggering mechanism for the fish kill. The Regional Water Board needs to increase efforts to explore whether rapid changes in flow are linked to pollution events and fish mortality. If the hypothesis is upheld by patterns in data, then the Regional Water Board should join discussions between the U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service, National Marine Fisheries Service and the Tribes on flow releases at Iron Gate dam to minimize algae bed shedding. A copy of Higgins (2009) is attached to these comments as Appendix 2 for the record. Appendix 3: Nutrient Dynamics in the Klamath As noted in comments on section 4.2.2 (Pollutant Source Area Loads: Copco 1 and 2 and Iron Gate Reservoirs) above, the TetraTech (2008) nutrient dynamics memorandum erroneously refers to May 2004 – May 2005 data from Kann and Asarian (2007), when in


35

fact the data are from May 2005 – May 2006. This should be corrected (searching through the document looking for “2004” will find all the instances). Appendix 5: Fish and Fishery Resources of the Klamath River Basin We suggest the following additions to the fish distribution maps (Figures 2, 3, 4) in Appendix 5 for the Shasta River basin: - Upper Shasta River above Dwinnell Reservoir: steelhead, coho, spring chinook (all three species extirpated) - Parks Creek: steelhead, coho, spring chinook (all three species present) - Yreka Creek: steelhead and coho (both species present, map shows only steelhead)


36

REFERENCES Asarian, E. and J. Kann. 2006. Klamath River Nitrogen Loading and Retention Dynamics, 1996-2004. Kier Associates Final Technical Report to the Yurok Tribe Environmental Program, Klamath, California. 56pp + appendices. Asarian, E. and J. Kann. 2009. (Draft) Nutrient Budgets Dynamics in Iron Gate and Copco Reservoirs, California, May 2005 – December 2007. Final Technical Report to the Karuk Tribe Department of Natural Resources, Orleans, CA. California Department of Forestry and Fire Protection (CDF). 2009. California Forest Practice Rules. Resource Management, Forest Practice Program. 328 pp. California State Water Resources Control Board (SWRCB). 2009. Item 7 on Board Agenda proposing Resolution on Timber Harvest, Grazing and Fire Suppression Oversight on National Forest System Lands. Agenda of August 4, 2009. de la Fuente, J. and D. Elder. 1998. The Flood of 1997 Klamath National Forest -Phase I Final Report. November 24, 1998. USDA Forest Service, Klamath National Forest, Yreka, CA. Dietrich, W.E., R.R. de Asua, J. Coyle, B. Orr, and M. Trso. 1998. A validation study of the shallow slope stability model, SHALSTAB, in forested lands of Northern California. Stillwater Ecosystem, Watershed & Riverine Sciences. Berkeley, CA. 59 pp. ESA Associates. 2008a. Scott River Watershed-wide Permitting Program Draft Environmental Impact Report. Performed for the California Department of Fish and Game by ESA Assoc. San Francisco, CA. 714 p. ESA Associates. 2008b. Shasta River Watershed-wide Permitting Program Draft Environmental Impact Report. Performed for the California Department of Fish and Game by ESA Assoc. San Francisco, CA. 658 p. Grant, G. 1988. The RAPID technique: a new method for evaluating downstream effects of forest practices on riparian zones. Gen. Tech. Rep. PNW-GTR-220. U.S. Department of Agriculture, Forest Service. Pacific Northwest Research Station. Portland, OR. 36p Higgins, P.T. 2009. Cautionary Note on Potential for Non-normative Water Quality Perturbations Related to Change in Flow Releases From Iron Gate Dam. Memo of March 24, 2009. By Patrick Higgins Consulting Fisheries Biologist, Arcata, CA. 11 p. Hill, B. 2009. Watersheds within the jurisdiction of the NCWQCB that are “over threshold’ for cumulative watershed impacts. Memo to Felice Pace. Spring 2009. USFS Region 5 Hydrologist, Vallejo, CA. 4 p.


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Hoopa Valley Tribe Environmental Protection Agency (HVTEPA). 2008. Water Quality Control Plan Hoopa Valley Indian Reservation. Approved September 11, 2002, Amendments Approved February 14, 2008. Hoopa Tribal EPA. Hoopa, CA. 285 p. Kann, J. 2006. Microcystis aeruginosa Occurrence in the Klamath River System of Southern Oregon and Northern California. Report for the Yurok Tribe Environmental Program and Fisheries Department, Klamath, CA by Aquatic Ecosystem Sciences, Ashland, OR. 26 p. Kann, J. 2008. Microcystin Bioaccumulation in Klamath River Fish and Freshwater Mussel Tissue: Preliminary 2007 Results. Technical Memorandum Prepared for the Karuk Tribe Department of Natural Resources. April 2008. Kann, J. and E. Asarian. 2005. 2002 Nutrient and Hydrological Loading to Iron Gate and Copco Reservoirs, California. Kier Associates Final Technical Report to the Karuk Tribe Department of Natural Resources, Orleans, California. 5p. +appendices. Kann, J. and E. Asarian. 2007. Nutrient Budgets and Phytoplankton Trends in Iron Gate and Copco Reservoirs, California, May 2005 - May 2006. Submitted to the State Water Resources Control Board, Sacramento, CA by the Karuk Tribe of California, Department of Natural Resources, Orleans, CA. Kann, J., and S. Corum. 2009. Toxigenic Microcystis aeruginosa bloom dynamics and cell density/chlorophyll a relationships with microcystin toxin in the Klamath River, 2005-2008. Technical Memorandum Prepared for the Karuk Tribe of California Department of Natural Resources. May 2009. http://www.karuk.us/dnr/pdf/wqdocuments/2008_Karuk_Toxic_Cyanobacteria_summary.pdf Karuk Tribe of California. 2008. Water Quality Report for 2008: Klamath, Salmon, Scott and Shasta Rivers and Bluff Creek. Karuk DNR, Orleans, CA. 75 p. Kier Associates. 1999. Mid-term evaluation of the Klamath River Basin Fisheries Restoration Program. Sausalito, CA. Prepared for the Klamath River Basin Fisheries Task Force. 303 pp. Kier Associates. 2005. Lower West Side Scott Shallow Landslide Hazard Maps. Performed under contract to the Quartz Valley Indian Reservation by Dr. Jan Derksen of Kier Associates on behalf of the Klamath Basin Water Quality Work Group. September 18, 2005. Kier Assoc., Sausalito, CA. 11 p. Kier Associates and National Marine Fisheries Service (NMFS). 2008. Updated Guide to Reference Values used in the Southern Oregon / Northern California Coho Salmon Recovery Conservation Action Planning (CAP) Workbook. Kier Associates, Blue Lake, CA and National Marine Fisheries Service, Arcata, CA. 31 pp.

http://www.karuk.us/dnr/pdf/wqdocuments/2008_Karuk_Toxic_Cyanobacteria_summary.pdf

http://www.karuk.us/dnr/pdf/wqdocuments/2008_Karuk_Toxic_Cyanobacteria_summary.pdf


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Mekebri A, G.J. Blondina, and D.B. Crane. 2009. Method validation of microcystins in water and tissue by enhanced liquid chromatography tandem mass spectrometry. J Chromatogr A. 1216(15):3147-55. Middle Klamath Watershed Council. 2006. Middle Klamath Refugia Characterization and Potential for Restoration. Report to Bella Vista Foundation. MKWC, Orleans, CA. North Coast Regional Water Quality Control Board. 2007. Water Quality Control Plan for the North Coast Region. Staff report adopted by the North Coast Regional Water Quality Control Board. Santa Rosa, CA. 201 p. PacifiCorp. 2004. Final License Application for the Klamath River Hydroelectric Project (FERC Project No. 2082). Portland, OR. Rehn, A.C., P.R. Ode, and C.P. Hawkins. 2007. Comparisons of targeted-riffle and reach-wide benthic macroinvertebrate samples: implications for data sharing in stream-condition assessments. North American Benthological Society. 26(2): 15-31. Royer, C.F. and A.P. Stubblefield. 2009. Preliminary Review Draft: Klamath River Basin Water Quality Monitoring Plan, Prepared for the Klamath Basin Water Quality Monitoring Coordination Group (KBWQMCG). Klamath Watershed Institute under contract to the North Coast Regional Water Quality Control Board. February 2009 Quartz Valley Indian Community. 2007. Comments on Klamath River Nutrient, Dissolved Oxygen, and Temperature TMDL Implementation Plan Workplan Outline for CA (NCRWQCB, 2007). Quartz Valley Indian Community, Fort Jones, CA. 30 pp. http://www.klamathwaterquality.com/documents/QVIC_Klamath%20TMDL%20Implementation%20Plan%20Comments_11.29.07.pdf Yurok Tribe. 2009. Comments on Review Draft Water Quality Restoration Plan for the Klamath River Basin in California: Draft Scoping for TMDL Implementation. Yurok Tribe, Klamath, CA. Snyder, J. O. 1931. Salmon of the Klamath River, California. California Division of Fish and Game, Fish Bulletin No. 34. Sacramento, CA. 121 pp. Tetra Tech. 2006. Technical approach to Develop Nutrient Numeric Endpoints for California. Prepared for U.S. Environmental Protection Agency (Contract No. 68-C-02-108-TO-111), and CA State Water Resources Control Board – Planning and Standards Implementation Unit. Lafayette, CA. 120 pp. Tetra Tech. 2008. Nutrient Dynamics in the Klamath. Prepared for U.S. EPA Region 9 and North Coast Regional Water Quality Control Board. February 12, 2008. Tetra Tech, Inc., Research Triangle Park, NC.

http://www.klamathwaterquality.com/documents/QVIC_Klamath%20TMDL%20Implementation%20Plan%20Comments_11.29.07.pdf

http://www.klamathwaterquality.com/documents/QVIC_Klamath%20TMDL%20Implementation%20Plan%20Comments_11.29.07.pdf


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U.S. Environmental Protection Agency (U.S. EPA). 1986a. Quality criteria for water 1986: EPA 440/5-86-001. Office of Water Regulations and Standards, Washington, DC. 477 p. U.S. Environmental Protection Agency. 1986b. Ambient Water Quality Criteria for Dissolved Oxygen. EPA 440/5-86-003. Office of Water. April, 1986. United States Environmental Protection Agency (USEPA). 2003. EPA Region 10 Guidance for Pacific Northwest State and Tribal Water Quality Standards. Region 10, Seattle, WA. EPA 910-B-03-002. 49pp. Accessed June 23, 2004. Available at: <http://www.epa.gov/r10earth/temperature.htm>. US Department of Agriculture, Forest Service (USFS). 1998. Elk River watershed analysis. Iteration 2.0. USFS, Pacific Northwest Region. Siskiyou National Forest. Powers Ranger District. Powers, OR. 192 pp. Available online at: <http://www.krisweb.com/kriskootenai/krisdb/html/krisweb/biblio/gen_usfs_powersrd_1998_elkriverwa.pdf> Van Kirk, R. and S. Naman. 2008. Relative effects of Climate and Water Use on Base-flow Trends in the Lower Klamath Basin. Journal of American Water Resources Association. August 2008. V 44, No. 4, 1034-1052. Washington Dept. of Ecology (WDOE). 2002. Evaluating Criteria for the Protection of Aquatic Life in Washington's Surface Water Quality Standards: Dissolved Oxygen. WDOE, Olympia, WA. 97 pp.

http://www.krisweb.com/kriskootenai/krisdb/html/krisweb/biblio/gen_usfs_powersrd_1998_elkriverwa.pdf

http://www.krisweb.com/kriskootenai/krisdb/html/krisweb/biblio/gen_usfs_powersrd_1998_elkriverwa.pdf

___________________________________________________________________________________________ QUARTZ VALLEY INDIAN RESERVATION – COMMENTS ON NCRWQCB’S DRAFT WORKPLAN OUTLINE FOR THE KLAMATH RIVER TMDL

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MEMORANDUM REPORT To: NCWQCB From: Quartz Valley Indian Community Date: November 29, 2007 Re: Comments on Klamath River Nutrient, Dissolved Oxygen, and Temperature TMDL Implementation

Plan Workplan Outline for CA (NCRWQCB, 2007) (If there are questions regarding any of the content in this memorandum, please contact Eli Asarian at [email protected] or 707-443-4743) On February 27, 2007 the members of the Klamath Basin Tribal Water Quality Work Group (Work Group) met with staff from the U.S. Environmental Protection Agency (EPA) and the North Coast Regional Water Quality Control Board (NCRWQCB) to discuss the on-going Klamath River Total Maximum Daily Load (Klamath TMDL) development effort. NCRWQCB staff shared a document entitled Klamath River Nutrient, Dissolved Oxygen, and Temperature TMDL Implementation Plan Workplan Outline for CA (NCRWQCB, 2007), which details their proposed strategy. The framework for the implementation plan is logical and comprehensive. The table appears here as Appendix 1, to which we have added a column of responses and comments by the Work Group. Klamath River nutrient pollution has been widely recognized since the 1950s (Phinney and Peak, 1960; CH2M Hill, 1985; Kier Associates, 1991). The adult salmon kill in the Klamath River in September 2002 (CDFG, 2003; Guillen, 2003), the chronic high mortality of juvenile salmon (Nichols and Foott, 2005), and the identification of problems with toxic algae in the Klamath Hydroelectric Project (KHP) reservoirs (Kann and Corum, 2006) all point to extremely serious Klamath River water quality issues. The Tribes are hopeful that the mainstem Klamath TMDL can avert the potential collapse of Klamath River salmon stocks by spurring measures to abate water pollution in the timeframe necessary for their recovery -- i.e. in the context of the Pacific Decadal Oscillation (Collison et al. 2003). In the Upper Klamath Basin, including Keno Reservoir, the Lost River sucker and shortnose suckers are, similarly, imperiled and will serve as indicators of whether water quality is, in fact, being restored, and whether TMDL implementation is proceeding as planned. Only major topics from the implementation table are discussed below. For the sake of brevity points from previous Klamath TMDL comments by Work Group members (QVIC, 2006; Yurok Tribe, 2006) are not repeated here. Those are, however, easily accessible on-line at the Work Group’s website: http://www.klamathwaterquality.com. The two most important points to be made in these comments are:

The restoration and maintenance of ecosystem function should be the principle around which TMDL implementation should be organized. This will entail removing, or setting back levees; restoring sinuosity in channelized stream reaches; expanding wetlands; and removing dams to provide free-flowing river reaches. Limits to road densities and timber


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harvests should be established in order to restore natural hydrologic and sediment supply regimes.

The NCRWQCB should prepare a proper implementation plan for the California portion of

the Lost River. The implementation plan recommended by U.S EPA in its March, 2007 Lost River TMDL (all EPA can do is “recommend” at this point) is inadequate. The Tribes request that the NCRWQCB either include Lost River implementation in the mainstem Klamath TMDL, or create a separate implementation plan for an improved Lost River TMDL.

Klamath River Interstate Water Pollution Challenge The North Coast Regional Water Quality Control Board relies on the cooperation of the Oregon Department of Environmental Quality (ODEQ), U.S. Environmental Protection Agency (U.S. EPA), Tribes and other land- and water management agencies to attain “delivery of water across the OR/CA boundary that meets CA water quality objectives” (NCRWQCB, 2007). If the water pollution control programs for Upper Klamath Lake, the tributaries to the lake, that for Lost River and Lower Klamath Lake do not succeed, then pollution of the mainstem and lower Klamath River will persist. Although NCRWQCB authority does not, of course, extend into Oregon, cooperative agreements with ODEQ, the U.S. EPA and other collaborators should be very clear in terms of which entity is responsible for which water quality restoration action, responsibility for the program of monitoring, and the timeline in which water quality recovery is to be accomplished. For example, the NCRWQCB should work with the U.S. EPA to insure that actions needed in the Lost River basin, including Lower Klamath Lake, are clearly defined in the forthcoming Lower Lost River TMDL (U.S. EPA, currently under review). Suckers are one of the most important and sensitive beneficial uses in the Upper Klamath Basin and Lost River, and measures taken to implement TMDLs need to be sufficient to recover these species. Such measures should follow the recommendations of the National Research Council (NRC, 2004). Upper Klamath Lake and its tributaries: Implementation of the Upper Klamath Lake TMDL (ODEQ, 2002) and related water quality management plans (ODA, 2004) rely heavily on voluntary measures. The TMDL’s monitoring requirements are vague and there is no required action for improving flows in tributaries above the lake to assist in water quality improvement. The Upper Klamath Basin Working Group (formerly known as the Hatfield Working Group) has been attempting to restore Upper Klamath Lake and its tributaries since 1996. Extensive areas of lakeside wetlands have been recreated near the mouth of the Williamson and Wood rivers and in Agency Lake. With regard to tributaries, substantial progress has been made in the lower Wood River (UKBWG, 2007), but the Working Group was only able to fund one third of the worthwhile conservation projects proposed in the 2006 grant competition (UKBWG, 2006). Additionally, the Sprague and Sycan River Watershed Assessment is stalled due to local resistance (UKBWG, 2006). Meetings have


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been hostile with regard to water management and some funding for conducting the analysis from the Oregon Watershed Enhancement Board may have to be turned back due to lack of progress. The Upper Basin Watershed Restoration Plan is also behind schedule and meeting similar resistance. Keno Reservoir: The Klamath TMDL must succeed in abating acute water quality problems in the reach extending from Keno Dam upstream to Klamath Falls. This reach can exhibit both nocturnal and diurnal anoxia for up to five weeks each year (Deas and Vaughn, 2006). Settlement negotiations related to the Klamath Hydroelectric Project (KHP) federal government relicensing process suggest that Keno Dam will be spared decommissioning, while the four KHP dams downstream of Keno Dam could be removed. If nutrient pollution problems are not resolved expeditiously in Keno Reservoir, the recovery of Klamath River salmon through dam removal could be severely confounded. The Klamath Straits Drain and other agricultural drainage sources to the Klamath River degrade water quality by discharging large quantities of untreated nutrient-rich, oxygen-poor water into Keno Reservoir (NRC 2004). The historic conditions of the area around Keno Reservoir are shown in Figure 1 and are described in NRC (2004) as follows:

“Between Lake Ewauna and Keno, the river meandered through a flat, marshy country (Henshaw and Dean 1915, p. 655) for about 20 miles before descending over a natural rock barrier that stretched across the river at Keno. Water in the river periodically backed up behind the reef at Keno and spread out upstream, flowing into Lower Klamath Lake through Klamath Straits.”

A vast wetland complex covered virtually the entire lowland area between Keno and Klamath Falls and was connected to Lower Klamath Lake (NRC, 2004). The height of the Keno Dam approximates the original bedrock sill at Keno that was blasted to drain wetlands and expand agricultural production (NRC, 2004). Today, however, extensive levees and dikes isolate the Klamath River from the remaining wetlands (Figure 2), denying their historic ability to buffer the river from receiving nutrients from storm runoff and agricultural discharges from adjacent farm fields. An issue that is underappreciated, yet critically important, is that channelization and diking impairs natural river processes that retain (i.e. remove from the water column) nutrients through denitrification, growth of attached algae, and the settling of organic matter. The result of channelization and diking in the upper Klamath River basin is, then, is much higher downstream nutrient loading than would have occurred historically. As described by Dodds and Bernot (2005):

“Several additional management methods that have not been regularly employed may prove to be useful in maximizing N retention and removal in lotic ecosystems. These include: 1) Maximizing substrata heterogeneity within the stream channel and creating backwaters where high rates of N flux can occur (for example, encouraging both nitrification and denitrification). … 3) Restoring channelized lotic ecosystems that inherently decrease the ability of the system to handle increased N loads. This restoration should include reversion to historical sinuosity, channel complexity, and connectivity to riparian wetlands as well as decreasing mean depth of the water column in the river channel.” (emphasis added)


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Figure 1. Photographs take on June 30, 1907 by the U.S. Bureau of Reclamation looking west from Wild Horse Butte towards Keno, prior to draining of the wetlands. Wild Horse Butte is a hill approximately one mile southeast of the present-day confluence of the Klamath Straits Drain and the Klamath River. These photographs are part of the Brown Album, a collection of 256 images of the early 1900s Klamath Basin, available online at the Klamath Waters Digital Library website.1

1 http://klamathwaterlib.oit.edu/cdm4/results.php?CISOOP1=all&CISOBOX1=brown%20album&CISOFIELD1=CISOSEARCHALL&CISOOP2=exact&CISOBOX2=&CISOFIELD2=CISOSEARCHALL&CISOOP3=any&CISOBOX3=&CISOFIELD3=CISOSEARCHALL&CISOOP4=none&CISOBOX4=&CISOFIELD4=CISOSEARCHALL&CISOROOT=all&t=a


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Figure 2. The impounded reach of the Klamath River near the town of Keno, Oregon shows how little functional riparian buffer area remains. Nutrients from farming activities flush directly into the river, promoting nutrient enrichment. Map from Google Earth. Keno Reservoir is U-shaped in cross-section with a low width-to-depth ratio and only a narrow band of shallow water along its margins. A waterbody with such morphological characteristics would be expected to have low nutrient retention (Dodds and Bernot, 2005; Biggs, 2000; Seitzinger, 2005). The historical channel and connected adjacent wetlands, by comparison, would have exhibited a much higher nutrient retention capability. As noted above, Keno Dam is likely to remain in place, but improvements could be made to the reservoir, such as adding fringing wetlands to increase complexity and nutrient retention. Deas and Vaughn (2006) recommend immediate action on a pilot scale to test the ability of wetlands to improve water quality in Keno Reservoir. The Klamath TMDL should make similar recommendations with the potential use of easements as a financial incentive. Subsequently, the NCRWQCB, ODEQ and U.S. EPA staff should work with the Bureau of Reclamation and the Upper Klamath Basin Working Group to make such restoration projects a priority. Klamath Straits Drain: Agricultural drain water from the federal government’s Klamath Reclamation Project, including the lower Lost River, Tule Sump and Lower Klamath Lake sub-basins are pumped into the Klamath River at the Straits Drain, near the California-Oregon border. Straits Drain water is a major contributor of nutrient pollution (QVIC, 2006; Yurok, 2006), including periodic pulses of unionized ammonia.


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In order to abate nutrient pollution from the Straits Drain, Tule Lake and Lower Klamath Lake need to be expanded. Mayer (2005) showed that nutrient loads released from the Lower Klamath Lake Wildlife Refuge were far less than incoming loads, though part of that was due to a decreased quantity of water outflow. Lower Klamath Lake is a peat bed that has the potential to be a giant nutrient sponge. The National Research Council (2004) called for its expansion to allow Lost River sucker and Shortnosed sucker recovery. The Draft Lower Lost River TMDL (U.S. EPA, in review) includes Lower Klamath Lake, and it should recommend expanding the lake as a step toward meeting TMDL implementation goals and to restoring the sucker species’ habitat beneficial use. If the habitat needs of sucker species were being met in the lower Lost River, Tule Lake and Lower Klamath Lake sub-basins, then there would not likely be water quality problems at the Straits Drain or in the Keno reach. Lower Lost River: The lower Lost River is confined by levees and consists largely of agricultural return water for much of the year (USFWS, 2001). Deliveries from Upper Klamath Lake through the A-Canal for the Klamath Project water users add substantially to the Lost River’s nutrient load. Ground water depletion has the potential to reduce contributions from spring sources in the few remaining Lost River reaches supporting suckers (USGS, 2005). Sucker distribution during summer is limited to impoundments and there is limited spawning access or success for the Lost River sucker population upstream of the Tule Sump (NRC, 2004). (See comments by Yurok Tribe, 2006, on Pre-Draft Lower Lost River TMDL). The draft Lost River California TMDL (U.S. EPA, in review) stresses the need to reduce non-point source pollution from agricultural operations. It does not recognize the need to restore ecosystem function and it fails to recommend restoration of riparian areas reconnecting the river with nutrient- stripping wetlands, nor expanding Tule Lake. It proposes a target of reducing nutrients by 50 percent, but provides no determination whether such reduced nutrient load will accomplish mainstem Klamath TMDL objectives for the Keno reach. Further, the Lower Lost TMDL designates the Klamath Basin Water Users Association as the lead organization for its plan implementation and makes no mention whatsoever of the interest in nor any role to be played by the Tribes in Lost River pollution abatement. Shaping a process controlled by the pollution source producers ensures gridlock and makes a science-driven adaptive management program extremely unlikely. NRC (2004) noted that despite huge expenditures of money on restoration, the USBR and the USFWS were not pursuing an adaptive management strategy for sucker recovery. Deas and Vaughn (2006) note that there is a substantial contribution of nutrients from the Lost River to the Klamath River through the Lost River Diversion Canal and the North Canal. Water quality problems with the Keno reach of the Klamath River cannot be solved without reducing pollution from the lower Lost River, Tule Lake, Lower Klamath Lake and the Straits Drain. We request, therefore, that the Klamath River and Lower Lost River TMDL implementation processes be combined.


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PacifiCorp Relicensing The Implementation Work Plan Outline (NCRWQCB, 2007) acknowledges important water quality issues that have come to light in the context of the proposed federal government relicensing of the Klamath Hydroelectric Project:

the role of the KHP reservoirs in nutrient pollution of the Lower Klamath River production of toxic algae in the Klamath River, and the nature and frequency of fish disease epidemics.

Work Group member Tribes have commented on KHP relicensing formally ever since 2004 ( see www.klamathwaterquality.com) and have contributed to Klamath River science by formulating nutrient budgets for the KHP reservoirs (Kann and Asarian, 2005) and free-flowing Klamath River reaches (Asarian and Kann, 2006a; Kann and Asarian, 2006). The Tribes have also documented chronic problems with the production of toxic algae in KHP reservoirs (Kann, 2005; 2006; Kann and Corum, 2006) and the persistence of toxic algae all the way to the Klamath River estuary (Yurok Tribe Environmental Program, 2006). PacifiCorp (2004; 2006; 2007) has countered that KHP reservoirs are nutrient sinks, or traps, that benefit Klamath River water quality, but the Work Group has demonstrated that there is a significant body of evidence that shows that the reservoirs are periodic sources of nutrients (Kann and Asarian, 2005; Asarian and Kann 2006a) and of toxic algae pollution (Karuk Tribe, 2007). The California State Water Resources Control Board and the Oregon Department of Environmental Quality have the responsibility to determine whether the proposed relicensing of the KHP by the federal government comports with the water quality standards and objectives of the States. Through the issuance – or withholding – of Clean Water Act Section 401 certificates, States may require water quality-related mitigation measures on the hydroelectric project. The Work Group Tribes have not yet been able to review the Klamath TMDL model ouputs in any detail, but if the TMDL water quality model suffers from the same issues as PacifiCorp’s water quality model (Asarian and Kann, 2006b) then the TMDL model may not provide an accurate tool for assessing the impacts of the KHP on Klamath River water quality and may, therefore, undermine the findings of the States’ 401 certifications. This would be a highly undesirable outcome, and is one to be scrupulously avoided. The evidence which demonstrates the links between the KHP reservoirs and incidences of fish disease outbreaks (Stocking and Bartholomew, 2004; in press); toxic algae blooms (Kann and Corum, 2006); and nutrient pollution (Kann and Asarian, 2005; Asarian and Kann, 2006) is substantial. Unless Klamath TMDL model performance can be significantly improved the Klamath TMDL should employ, instead, a weight of evidence approach in assessing these water quality-related problems. If the best scientific information available indicates that dam removal would improve Klamath River water quality, the Klamath TMDL should so state. Monitoring plans for the TMDL’s implementation related to the KHP should include both with- and without-dam contingencies.


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Rangeland Management Although direct livestock grazing impacts on mainstem Klamath River riparian zones are generally limited, there is intensive stream-side grazing just above Horse Creek. Ironically, some Klamath River riparian areas below Iron Gate Dam have been deforested, after having been retired as rangelands, for residential and recreational uses. Above Iron Gate Dam, substantial tributary impacts from grazing still occur in Shovel and Spencer creeks. Below the KHP, the riparian zones of the Bogus, Cottonwood, Willow, and Horse Creek tributaries have all been altered by livestock grazing. Bogus Creek is spring fed and has served as a refugia for salmon and steelhead (Kier Associates, 1999), but there are indications that water temperature increases occurred there between 1996 and 1999. Diversion for stock water and pasture irrigation may be contributing more to thermal problems there are direct impacts to the riparian zone from grazing. The Klamath TMDL should foster the development of farm and ranch plans, including the identification of sensitive riparian habitats on both the mainstem Klamath River and it tributaries. The TMDL should advance the policy of acquiring sensitive habitats, i.e, through a program of conservation easement acquisition. Such a program would promote riparian health, improve fish habitat and increase riparian nutrient filter capability while improving the economic viability of cattle ranching. Public land grazing is a lesser issue and can be addressed through an updated MOU between the NCRWQCB and the responsible federal agencies (see public land timber harvest section below). Streamflow Issues The flow of the Klamath River is controlled in large part by the U.S. Bureau of Reclamation (BOR), which releases water from Upper Klamath Lake at Link River Dam. Even so, the Klamath TMDL should include a discussion of the findings of the Hardy and Addley (2001) that flow releases at Iron Gate Dam should never fall below 1,000 cfs to maintain healthy downstream conditions for Pacific salmon. According the U.S Bureau of Reclamation, the Klamath Project Operations Plan for 2007 has adopted flow levels similar to those recommended by Hardy and Addley (2001) as a result of U.S. District Court ruling CIV. NO CO2-2006 SBA (BOR, 2007). It is encouraging to see clear language in the Klamath TMDL implementation outline (NCRWQCB, 2007) regarding the need to protect and restore adequate flow to protect beneficial uses, e.g., “Work with State Division of Water Rights to establish a flow objective that addresses thermal refugia protection, fish disease, and algae blooms.” The NCRWQCB should also consider exerting its direct authority in the Klamath TMDL to increase flows, where water quality impairment can best be abated by improving flows (U.S. Supreme Court, 1994). The Karuk Tribe Department of Natural Resources (Soto and Hentz, 2003) has been conducting flow surveys of Middle Klamath River tributaries that serve as summer refugia for juvenile salmon


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and steelhead (MKWC, 2007). The Klamath TMDL should reference these data and make clear statements about the need to maintain flows in streams that serve as refugia. The SWRCB Water Rights Division needs to explicitly recognize the need to limit further surface and ground water diversion in important Klamath River tributaries and along the mainstem river. The U.S. EPA (2003) points out the importance of maintaining the spatial distribution of thermal refugia for the conservation of Pacific salmon species. The Klamath TMDL must prevent alteration of hydrologic conditions by timber harvest and road construction activities (Jones and Grant, 1996) in Klamath Basin tributary watersheds. Such alteration can increase the frequency of damaging peak flood flows and decrease summer base flows (see below). The worst problems of this nature are in tributaries below Weitchpec, where 17 of 23 streams lose their surface flow in late summer before they can reach the Klamath River as a result of cumulative effects from timber harvest (Kier Associates, 1999). The Klamath TMDL should also recognize the role of wetland restoration as a potential mechanism for water storage and recommend increasing wetlands for water quality, fisheries and streamflow benefits. The NCRWQCB staff should resist endorsing “water bank” subsidies in the Klamath TMDL that must be paid every year to farmers and ranchers. Instead the TMDL should favor payments for the retirement of water rights, particularly on marginally productive agricultural land or in those sensitive riparian zones where conservation easements are needed. Private Timberland Management The NCRWQCB (2007) has laid out very clear objectives to bring timber harvest on private lands into compliance with the TMDL goals of reducing water pollution and maintaining tributary refugia. This is a very positive direction. The key to successful implementation, however, is to set explicit thresholds for road density, rates of timber harvest and disturbance of unstable slopes or soil types. Guidance on limits of prudent risk for logging and road building, based on the scientific literature, have been offered in Table 5 of previous Klamath River TMDL comments provided by the Quartz Valley Indian Community (2006). As noted by Kier Associates (1999), highly erodible decomposed granitic terrain runs through the Middle Klamath River Basin, resulting in widespread areas of high erosion risk, particularly in the Beaver and Horse Creek watersheds. Lower Klamath tributaries have extremely steep terrain and disturbance of areas at high risk of producing debris torrents should be avoided. The Work Group recommends the use of the shallow landslide stability model (SHALSTAB) (Dietrich et al., 1998) as a tool for preliminary identification of these high risk areas (see Kier Associates, 2005). The Klamath TMDL should recommend removing the most unstable areas from timber harvest rotations. The Klamath TMDL implementation plan should include studies exploring watershed disturbance rates, examining the location of roads and timber harvest activity, and resulting changes in channel conditions that contribute to stream warming. Increased peak flows resulting from extensive timber


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harvest and road networks can fill pools and change the width-to-depth ratio of streams; this is a particular concern in watersheds which lie substantially in the transient snow zone (Jones and Grant, 1996). The U.S.F.S. has recognized high cumulative effects risk in Beaver Creek and Horse Creek because very high rates of timber harvest on private lands within those watersheds (Figure 3).

Figure 3. This photo of the Horse Creek watershed shows widespread clear cuts in the transient snow zone that pose high cumulative effects risk. Photo courtesy of and copyright by Michael Hentz. Public Land Timber Harvest The Klamath TMDL workplan outline (NCRWQCB, 2007) invokes the 1981 Management Agency Agreement (MAA) between the SWRCB and federal land management agencies, but notes that an updated Memorandum of Understanding (MOU) is needed with the “USFS and BLM that addresses road maintenance and road density in addition to timber harvest BMPs that protect thermal refugia and riparian function.” The January 1997 storm caused 437 miles of stream channel scour. De la Fuente and Elder (1998) found that rates of land-sliding were much greater on harvested lands (e.g. see Figure 4). This argues strongly for an updated MOU. The Salmon River TMDL (NCRWQCB, 2005b) recognized that the Salmon River Subbasin Restoration Strategy: Steps to Recovery and Conservation of Aquatic Resources (Elder et al., 2001) is the equivalent of a TMDL implementation plan. The Klamath TMDL should, similarly, reference the several USFS


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watershed analyses (SRNF, 2003b; KNF 2000; 2003a) and road network studies (SRNF, 2003a; KNF, 2002) and recommend the funding actions from them to reduce road-related erosion. The ultimate goal should be to reduce road networks sufficiently that annual maintenance becomes practical and widespread road bed failures in major storm events can be prevented.

Figure 4. This lower Westside Scott River map shows the Kelsey Creek watershed, Klamath National Forest timber harvests in the 1980’s and 1990’s (blue) and the occurrence of flood damage sites (the pink triangles). The red lines are channels scoured by debris torrents. Lower Kelsey Creek warmed significantly because of these changes. A USGS 1996 orthophoto serves as the backdrop. From QVIC (2006). The older style of even-age timber management on USFS lands has left a legacy of high cumulative watershed impacts and fire risks. The Klamath TMDL should recommend that future public land timber management restore the diverse stand age that promotes a hydrologic function more closely resembling the normal range of variability in which salmon and steelhead co-evolved (QVIC, 2006). Irrigated Agriculture The Draft Implementation Work Plan Outline (NCRWQCB, 2007) addresses the major irrigated agriculture issues, but leaves flow protection to voluntary measures, only. These will not likely work to protect and restore the bneficial uses of the basin’s water resources (see “Streamflow Issues”, above). The NCRWQCB (2007) recognizes that “wetlands can be used to decrease nutrient concentrations.” As noted above, the Klamath TMDL needs to specifically address riparian wetland restoration along the Keno Reservoir, and to seek similar action in the Lower Lost River, Tule Lake and Lower Klamath Lake sub-basins in order to reduce pollution from the Klamath Straits Drain. Waiver of waste discharge requirements should not be granted landowners that lack farm or ranch plans that provide water conservation and riparian mitigation strategies. The NCRWQCB (2007)


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notes that funds for conservation measures are needed for TMDL implementation. Staff should consider recommending an economic study by NRCS to explore more salmon-friendly and sustainable agricultural methods, such as production of value-added products like organic grains or produce that have low water use requirements. Fish Diseases Fish disease studies by Oregon State University (Stocking and Bartholomew, 2004; in press) show that there is a concentration below Iron Gate Dam of the polychaete Manayunkia speciosa that serves as the intermediate host for Ceratomyxa shasta, the Klamath River’s most widespread and virulent fish disease. Linkage between this disease and KHP operations is clear in that:

• Flow regulation below Iron Gate allows the accumulation of fine organic sediment and beds of the algae Cladophora to proliferate, providing ideal substrate for Manayunkia,

• Spores of C. shasta are abundant below Iron Gate Dam as chinook salmon carcasses accumulate because access to upstream spawning areas is blocked, and

• At some times during the year, KHP reservoirs contribute to nutrient pollution in the lower Klamath River that stresses juvenile salmonids and decreases their resistance to disease.

Klamath River salmonids have co-evolved with C. shasta, but epidemics are killing hundreds of thousands of juvenile salmonids annually (Nichols and Foott, 2005). The removal of KHP reservoirs could reduce nutrient pollution, permit scour that would reduce Manayunkia habitat, enable spawner disbursement, reducing the present concentrated supply of C. shasta spores, and allow access to cold water spring areas above the current dam sites. The Klamath TMDL implementation outline (NCRWQCB, 2007) discusses manipulating flows to increase scour, to decrease water temperatures and thereby to reduce disease incidence. The currently available science suggests, however, that it may not be possible to abate the conditions which exacerbate Klamath River salmon disease epidemics without dam removal, and the Klamath TMDL make this point clear. Algae Blooms (See, also, “PacifiCorp Relicensing”, above) KHP reservoirs harbor Aphanizomenon flos-aquae, a nitrogen-fixing blue-green algae. The toxic algae Microcystis Aeruginosa proliferates in Copco and Iron Gate reservoirs. These reservoirs produce the high concentrations of Microcystis observed in the lower river in recent years (Kann and Corum, 2006). The Yurok Tribe Environmental Program (2006) measured microcystin toxins in Klamath River samples all the way to the estuary and even found trace amounts in the liver of steelhead half-pounders. Recommendations for limits of toxic algae and toxin levels (NCRWQCB, 2007) are appropriate, but control of the problem is not likely feasible without KHP dam removal.


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County and State Roads Counties in northwestern California have been working cooperatively to reduce erosion from their road systems and to improve fish passage at road-stream crossings (Trinity County Public Works, 2003). The Klamath TMDL should acknowledge county efforts and specifically recommend funding for defined erosion control efforts consistent with TMDL implementation objectives. The NCRWQCB has already started cooperative efforts with Siskiyou County to reduce erosion from its road network as part of the Scott River TMDL (NCRWQCB, 2005a). These efforts should be expanded to include Humboldt County. Highway 96 parallels the Klamath River and has been a major source of sediment over the years. The TMDL should acknowledge improved practices by CalTrans with regard to hauling sediment from landslides to stable areas, as opposed to the old practice of side-casting debris into the river. In recognition of the importance of fish access to Middle Klamath River tributary refugia (MKWC, 2007), the Klamath TMDL should recommend that CalTrans fix barriers associated with Highway 96, on a priority basis. Chapter 589, State Statutes of 2005 requires CalTrans to provide CDFG an accounting of fish barriers at State highway crossings throughout the state and an annual update on measure being taken to remediate them. NCRWQCB staff should pursue that initial report (the Tribes have inquired as to its status) and, working with DFG, Tribal biologists and others knowledgeable about Klamath River basin fish barriers, assure that the CalTrans accounting in the Klamath basin is complete and that remediation of Klamath basin barriers is given high priority by CalTrans. Recovery of Endangered Fishes The NCRWQCB work plan (2007) identifies coho salmon recovery measures, but does not appear to address other at-risk Pacific salmon species, such as spring chinook salmon. We expect that the final Klamath TMDL will adequately address recovery of all Pacific salmon (QVIC, 2006) and sucker species (NRC, 2004). The prospect for full recovery of Pacific salmon to fishable levels that meet Tribal needs are much better if actions are taken swiftly before the Pacific Decadal Oscillation switches to unfavorable ocean conditions and a drier climatic regime (Hare et al., 1999) some time between 2015 and 2025 (Collison et al., 2003). Salmon stocks may not be recoverable if freshwater habitat restoration is not well advanced before the next switch of the PDO (Collison et al., 2003). TMDL implementation timelines, however, can stretch over four or five decades. Although not listed under the ESA, the last viable population of spring chinook salmon is in the Salmon River and is at risk of extinction due to extremely low adult returns (Kier Associates, 1999). The original Klamath River meta-population of spring chinook salmon included the upper Klamath, Scott, Shasta and Salmon river sub-populations. Rieman et al. (1993) point out that “the diversity of local populations in variable environments conveys stability to the larger meta-population.”


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Long term viability of Klamath River spring chinook relies on restoring populations in the upper Klamath, Shasta and Scott rivers in the event that the Salmon River population is lost due to stochastic events or genetic drift (Rieman et al., 1993). KHP dam removal would enable spring chinook access to important thermal refugia in the springs below the current site of J.C. Boyle Dam. Although the at-risk status of Lost River and short-nosed suckers has been recognized since 1988 (USFWS, 1993), according to NRC (2004) “USFWS and the Ecosystem Restoration Office do not appear to have an operational recovery plan for the two sucker species.” The final Klamath TMDL should recognize sucker species as water quality indicators in upper basin reaches and provide an expected time-frame for recovery. Implementation Must Have Wetland Restoration Emphasis Mayer’s (2005) research on nutrient retention in the Lower Klamath Lake Wildlife Refuge suggests that wetland restoration could play a major role in improving Klamath River water quality. The Klamath TMDL should endorse the recommendations of Deas and Vaughn (2006):

“Consider implementing a pilot project to assess organic matter removal potential of treatment wetlands with a small scale project adjacent to the Klamath River or in neighboring areas. Such projects would be invaluable investigations not only into the ability of wetlands to process organic matter, but also to determine the best methods to implement, maintain, and operate such a system.”

Deas and Vaughn (2006) focused their analyses on the use of wetlands for organic matter removal, with the primary goal of improving dissolved oxygen conditions in Keno Reservoir. Consistent with their stated goals, Deas and Vaughn (2006) recommended wetlands with a relatively short residence time (i.e., the amount of time that incoming water remains in the wetland before exiting) of approximately four days. This approach would reduce total nutrient concentrations by removing (settling) nutrients contained in particulate organic matter; however, the use of larger wetlands with longer residence times offers significantly more potential for removing dissolved inorganic forms of nitrogen (e.g. ammonia and nitrate). To achieve these longer residence times, wetlands would have to be larger to treat the same quantity of flow, but their effluent would have greatly reduced nitrogen concentrations. Additional design elements such as open water (not completely vegetated) zones are also necessary to maximize nitrogen removal through denitrification (U.S. EPA 1993; 1999; 2000). Because wetlands are rich living systems that generate their own internal nutrient loads, relative (i.e. percentage) removal efficiencies of treatment wetlands are most effective when influent concentrations are highest. To illustrate with a hypothetical example, in a municipal wastewater treatment system where influent total nitrogen concentrations are 50 mg/L a properly designed wetland could remove 90 percent of the incoming nitrogen, i.e., resulting in effluent concentrations of 5 mg/L. If influent concentrations were 4 mg/L (typical concentrations at Link Dam in mid-summer), however, then a wetland may only be able to reduce concentrations to 50 percent, i.e, down to 2 mg/L.


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For this reason, some people may say that nutrient concentrations are too low in the Klamath River for treatment wetlands to be able to effectively remove nutrients. This may be a concern; however, evidence from other rivers with similar or even lower nutrient concentrations than the Klamath shows that wetlands can, in fact, be effective. For example, constructed wetlands have been used successfully to reduce nutrient concentrations in the Des Plaines River in Illinois, where nitrogen concentrations are similar to those in the upper Klamath River. Water is diverted from the Des Plaines, routed through constructed wetlands, and then returned to the river (U.S. EPA, 1993). On an annual basis, the wetlands removed 78-95 percent of the nitrate and 54-75 percent of the total nitrogen received (Phipps and Crumpton, 1994). It is also important to note that due to seasonal climate differences, nutrient removal efficiencies vary at Des Plaines and other wetland systems. Nitrate reductions are highest in summer because de-nitrification (the conversion of nitrate to inert amospheric nitrogen) rates are temperature-driven. In many wetlands, nutrients can be released in the fall when plants senesce, or in spring when decomposition rates increase as temperatures begin to rise (U.S. EPA 2000); however, nutrient release during these periods may not be detrimental because water quality in the Klamath River is less impaired during those times of the year Monitoring Should Support Adaptive Management The NRC (2004) pointed out that, despite huge expenditures and numerous restoration programs and restoration groups, that there is no effort toward adaptive management. The final Klamath TMDL should explicitly define monitoring activities needed to gauge the success of water pollution abatement efforts, the methods of data storage, and defined time periods for evaluation. Work Group member Tribes are ready to engage in discussions about long-term monitoring needs. Deas and Vaughn (2006) recommend monitoring to assess the efficacy of wetland restoration in reducing nutrient pollution, which the Klamath TMDL should explicitly endorse. Work Group member Tribes see the need for a coordinated information system of reliable scientific data to facilitate participatory co-management with state and federal agencies. Member Tribes unsuccessfully sought Prop 50 funds to provide equipment and technical support (Hoopa Tribe, 2005) to provide a hub for updating the Klamath Resource Information System (KRIS). KRIS was created, with SWRCB/NCRWQCB funding, by the Klamath River Basin Fisheries Task Force to gauge restoration success. Likewise, KRIS has been supported by the Trinity River Restoration Program. It would make an ideal mechanism with which to support the tracking of TMDL implementation success.

REFERENCES Asarian, E. and J. Kann. 2006a. Klamath River Nitrogen Loading and Retention Dynamics, 1996-

2004. Kier Associates Final Technical Report to the Yurok Tribe Environmental Program, Klamath, California. 56pp + appendices.


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Asarian, E. and J. Kann. 2006b. Technical Memorandum: Evaluation of PacifiCorps’s Klamath River Water Quality Model Predictions for Selected Water Quality Parameters. Prepared by Kier Associates and Aquatic Ecosystem Sciences for the Yurok Tribe Environmental Program, Klamath, California. 32 pp.

Biggs, B.J.F. 2000. New Zealand Periphyton Guideline: Detection, Monitoring, and Managing Enrichment of Streams. Prepared for Ministry of Environment. NIWA, Christchurch. Available online at: <http://rd.tetratech.com/epa/Documents/Periphyton.zip> Accessed 10 June 2007.

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Collison, A., W. Emmingham, F. Everest, W. Haneberg, R. Marston, D. Tarboton, and R. Twiss. 2003. Phase II report: Independent Scientific Review Panel on sediment impairment and effects on beneficial uses of the Elk River and Stitz, Bear, Jordan and Freshwater creeks. Authored by the Humboldt Watersheds Independent Scientific Review Panel under the auspices of the North Coast Regional Water Quality Control Board. Santa Rosa, CA. 95 pp. Available online at: <http://www.krisweb.com/biblio/hum_swrcb_collison_2003_phaseiiisrp.pdf> Accessed 10 June 2007.

Deas, M.L. and J. Vaughn. 2006. Characterization of Organic Matter Fate and Transport in the Klamath River below Link Dam to Assess Treatment/Reduction Potential. Prepared for the U.S. Bureau of Reclamation, Klamath Falls, OR. 167. p.

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Bernot, M. J. and W. K. Dodds. 2005. Nitrogen retention, removal, and saturation in lotic ecosystems. Ecosystems 8:442-453. Available online at: <http://www.biol.vt.edu/faculty/webster/linx/linx2pdfs/bernot%20and%20dodds%20ecosystems%202005.pdf> Accessed 01 March 2007

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Guillen, G. 2003. Klamath River fish die-off, September 2002: Causative factors of mortality. Report number AFWO-F-02-03. U.S. Fish and Wildlife Service, Arcata Fish and Wildlife Office. Arcata, CA. 128 pp.


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Hardy, T. B. and R. C. Addley. 2001. DRAFT. Evaluation of interim instream flow needs in the Klamath River: Phase II. Performed under contract to U.S. DOI by the Institute for Natural Systems Engineering, Utah Water Research Laboratory, Utah State University, Logan, UT. 315 p.

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Jones, J.A. and G.E. Grant. 1996. Peak flow response to clear-cutting and roads in small and large basins, Western Cascades, Oregon. Water Resources Research, April 1996. Vol. 32, No. 4, Pages 959-974.

Kann, J. 2005. Copco/Irongate Reservoir Toxic Cyanobacteria Results, Aug-Sep. Technical Memoranda to Karuk Tribe, NCWQCB and SWQCB.

Kann, J. 2006. Microcystis aeruginosa Occurrence in the Klamath River System of Southern Oregon and Northern California. Prepared for the Yurok Tribe Environmental and Fisheries Programs by Aquatic Ecosystem Sciences LLC, Ashland, Oregon.

Kann, J. and E. Asarian. 2005. 2002 Nutrient and Hydrologic Loading to Iron Gate and Copco Reservoirs, California. Kier Associates Final Technical Report to the Karuk Tribe Department of Natural Resources, Orleans, California. 59pp + appendices.

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Kann, J. and S. Corum. 2006. Summary of 2005 Toxic Microcystis aeruginosa Trends in Copco and Iron Gate Reservoirs on the Klamath River, CA. Prepared by Aquatic Ecosystem Sciences and the Karuk Tribe Department of Natural Resources for the Karuk Tribe, Orleans, California. 35 pp.

Karuk Tribe. 2007. Causes and effects of nutrient conditions in the Upper Klamath River and PacifiCorp’s response to comments from various stakeholders on September 2006 FERC DEIS for the Klamath Hydroelectric Project. FERC License 2082-027, Operated by PacifiCorp. Filed on April 12, 2007. 32 p.

Kier Associates. 1991. Long Range Plan for the Klamath River Basin Conservation Area Fishery Restoration Program. U.S. Fish and Wildlife Service, Klamath River Fishery Resource Office. Yreka, CA. 403 pp.

Kier Associates. 1999. Mid-term evaluation of the Klamath River Basin Fisheries Restoration Program. Sausalito, CA. Prepared for the Klamath River Basin Fisheries Task Force. 303 pp.

Kier Associates. 2005. Lower Westside Scott River Shallow Landslide Hazard Maps. Performed under contract to the Quartz Valley Indian Community by Dr. Jan Derksen of Kier Associates on behalf of the Klamath Basin Water Quality Work Group. Kier Associates, Arcata, CA. 11 p.


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Mayer, T.D. 2005. Water Quality Impacts of Wetland Management in the Lower Klamath National Wildlife Refuge, Oregon and California, USA. Wetlands 25: 697-712.

Middle Klamath Watershed Council (MKWK). 2007. Middle Klamath Creek Mouth Assessments,

2006-2007. Preliminary report to the Bella Vista Foundation, MKWC, Orleans, CA. 18 p. plus appendices.

National Research Council (NRC). 2004. Endangered and Threatened Fishes in the Klamath River Basin: causes of decline and strategies for recovery” National Academies Press. 424 pp.

Nichols, K. and J. Scott Foott. 2005. FY2004 Investigational report: Health Monitoring of Juvenile Klamath River chinook Salmon. U.S. Fish & Wildlife Service California-Nevada Fish Health Center, Anderson, CA.

North Coast Regional Water Quality Control Board. 2001. Water Quality Control Plan for the North Coast Region. Staff report adopted by the North Coast Regional Water Quality Control Board on June 28, 2001. Santa Rosa, CA. 124 p.

North Coast Regional Water Quality Control Board (NCRWQCB). 2005a. Action Plan for the Scott River Watershed Sediment and Temperature Total Maximum Daily Loads. NCRWQCB, Santa Rosa, CA. 4 p.

North Coast Regional Water Quality Control Board (NCRWQCB). 2005b. Salmon River, Siskiyou County, California, Total Maximum Daily Load for Temperature and Implementation Plan. Adopted June 22, 2005, NCRWQCB Resolution No. R1-2005-0058. NCRWQCB, Santa Rosa, CA.

North Coast Regional Water Quality Control Board. 2007. Draft Klamath River Nutrient, Dissolved Oxygen, and Temperature TMDL Implementation Plan Workplan Outline for CA. NCRWQCB, Santa Rosa, CA.

Oregon Department of Agriculture (ODA). 2004. Klamath Headwaters Agricultural Water Quality Management Area Plan. assistance from the Klamath Headwaters Local Advisory Cmte and the Klamath Soil and Water Conservation District. ODA, Portland, OR. 41 p.

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Oregon Water Resources Department (ODWR). 2004. State of Oregon’s Comments on PacifiCorp’s Klamath Hydroelectric Project (FERC # 2082) Final License Application and Additional Study Requests. Comments from OWRD for all Oregon agencies, Salem, OR. 214 p.

PacifiCorp. 2004. Final License Application for the Klamath River Hydroelectric Project (FERC Project No. 2082). Portland, OR.

PacifiCorp. 2006. Appendix B: Causes and Effects of Nutrient Conditions in the Upper Klamath River, Klamath Hydroelectric Project (FERC Project No. 2082). PacifiCorp, Portland, Oregon.


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PacifiCorp. 2007. PacifiCorp’s Responses to Comments from Various Stakeholders on the September 2006 FERC DEIS for Hydropower License for the Klamath Hydroelectric Project (FERC Project No. 2082). PacifiCorp, Portland, Oregon.

Phinney, H. and C.H. Peek. 1960. Klamath Lake, an instance of natural enrichment. Transactions of the Seminar on Algae and Metropolitan Wastes, April 27-29, 1960. U.S.

Public Health Service, Robert A. Taft Sanitary Engineering Center, Cincinnati, OH. 6 p.

Phipps, RG, WG Crumpton. 1994. Factors affecting nitrogen loss in experimental wetlands with different hydrologic loads. Ecological Engineering. Vol. 3, no. 4, pp. 399-408.

Quartz Valley Indian Community. 2006. Comments Concerning the Klamath River TMDL Approach and Progress to Date. Memo to the U.S. EPA and North Coast Regional Water Quality Control Board of August 15, 2006. Quartz Valley Indian Reservation, Ft. Jones, CA. 35 p. www.klamathwaterquality.com/QVIC_LowerKlamath_TMDL_Comments_08.15.06.pdf

Rieman, B., D. Lee, J. McIntyre, K. Overton, and R. Thurow 1993. Consideration of Extinction Risks for Salmonids. As FHR Currents # 14. US Forest Service, Region 5. Eureka, CA. 12 pp.

Soto, T. and M.M. Hentz. 2003. DRAFT Middle Klamath Basin Fisheries Recovery Plan. Prepared by the Karuk Tribe of California Natural Resources Division for the Klamath River Basin Fishery Task Force. 42 p.

Stocking, R.W. and J.L. Bartholomew. 2004. Assessing links between water quality, river health and Ceratomyxosis of salmonids in the Klamath River system. Oregon State University. Corvallis, Oregon. 5 pp.

Stocking, R. W. and Bartholomew, J. L. (In Press). Distribution and habitat characteristics of Manayunkia speciosa and infection prevalence with the parasite, Ceratomyxa shasta, in the Klamath River, OR-CA, USA. Submitted for publication in the Journal of Parasitology.

Trinity County Public Works Department. 2003. Five County Road Erosion Assessment and Salmonid Conservation Plan. Performed with funding from CDFG and SB-271. TCPD, Weaverville, Ca.

U.S. Bureau of Reclamation (BOR). 2007. Klamath Project Operations Plan for 2007. Memo from U.S. BOR, Klamath Falls, OR. 9 p. http://www.usbr.gov/mp/kbao/operations/FINAL_2007_Ops_Plan_04-09-07.pdf

U.S. Environmental Protection Agency (U.S. EPA). 1993. Contructed Wetlands for Wastewater Treatment and Wildlife Habitat: 17 Case Studies. EPA832/R-93/005. U.S. EPA. Available online at: <http://www.epa.gov/owow/wetlands/construc/> Accessed 07 June 2007.

U.S. Environmental Protection Agency (U.S. EPA). 1999. Free Water Surface Wetlands for Wastewater Treatment: A Technology Assessment. EPA832/S-99/002. U.S. EPA. Available online at: <http://www.epa.gov/owow/wetlands/pdf/FW_Surface_Wetlands.pdf> Accessed 07 June 2007.

U.S. Environmental Protection Agency (U.S. EPA). 2000. Contructed Wetlands Treatment of Municipal Wastewaters. EPA/625/R-99/010. U.S EPA, Office of Research and


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Development, Cincinnati, Ohio. Available online at: <http://www.epa.gov/owow/wetlands/pdf/Design_Manual2000.pdf> Accessed 07 June 2007

U.S. Environmental Protection Agency (US EPA). 2003. EPA Region 10 Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards. EPA 910-B-03-002. Region 10 Office of Water, Seattle, WA.

U.S. Environmental Protection Agency. In review. Lost River California Total Maximum Daily Load: Nitrogen and Biochemical Oxygen Demand, Dissolved Oxygen and pH Impairments. Public review draft released March 2007. U.S. EPA Region 9, San Francisco, CA. 57 p. plus appendices.

U.S. Fish and Wildlife Service (USFWS). 1993. Lost River (Deltistes luxatus) and Shortnose (Chasmistes brevirostris) Sucker recovery plan. Prepared by Kevin Stubbs and Rolland White. Portland, OR. 80 pp. Available online at: <http://www.krisweb.com/biblio/klamath_usfws_stubbsetal_1993.pdf>

U.S. Fish and Wildlife Service (USFWS). 2001. Biological/Conference Opinion Regarding the Effects of Operation of the Bureau of Reclamation's Klamath Project on the Endangered Lost River Sucker (Deltistes luxatus), Endangered Shortnose Sucker (Chasmistes brevirostris), Threatened Bald Eagle (Haliaeetus leucocephalus), and Proposed Critical Habitat for the Lost River/Shortnose Suckers. U.S. Fish and Wildlife Service, Klamath Falls Fish and Wildlife Office, Klamath Falls, OR.

U.S. Forest Service, Klamath National Forest (KNF). 2000. Thompson, Siead and Grider Creek Watershed Analysis. Klamath National Forest, Yreka, CA.

U.S. Forest Service, Klamath National Forest (KNF). 2002. Forest-wide Road Assessment. Klamath

National Forest Supervisors Office, Yreka, CA. 91 p. U.S. Forest Service, Klamath National Forest (KNF). 2003a. Horse Creek Watershed Analysis.

Klamath National Forest, Yreka, CA. U.S. Forest Service, Six Rivers National Forest (SRNF). 2003a. Six Rivers National Forest Roads

Analysis, Version 1.0. USFS SRNF, Eureka, CA. 120 pp. U.S. Forest Service, Six Rivers National Forest (SRNF). 2003b. Lower-Middle Klamath

Watershed Analysis. Prepared by USFS, Pacific Southwest Region, Six River National Forest, Orleans Ranger District. Eureka, CA. 389 pp.

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Review from a Hydrologic Perspective. Performed under contract to U.S. BOR, Klamath Falls, OR by the USGS, Portland, OR. 98 p. Available online at: www.usbr.gov/mp/kbao/docs/Final_USGS_Assessment_of_Water_Bank.pdf

US Supreme Court. 1994. PUD No 1 of Jefferson County and City of Tacoma v. Washington Department of Ecology. 511 U.S. 700, 114 S. Ct. 1900, 128 L. Ed 2d 716, 1994. Decision No. 92-1911, May 31, 1994.

Upper Klamath Basin Working Group (UKBWG). 2006. Meeting notes from November 30, 2006. Posted at: http://www.fs.fed.us/r6/frewin/projects/ukbwg/notes/06-11-30.shtml


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Upper Klamath Basin Working Group (UKBWG). 2007. Meeting notes from January 18, 2007. Posted to the Internet at: http://www.fs.fed.us/r6/frewin/projects/ukbwg/notes/07-01-18.shtml

Yurok Tribe. 2006. Memo re: Yurok Tribe comments on Lower Lost River TMDL. From Kevin McKernan, Yurok Tribe Environmental Program Director, to Noemi Emeric of U.S. Environmental Protection Agency. 29 p. http://www.klamathwaterquality.com/lower%20lost%20comments_Yurok.pdf

Yurok Tribe Environmental Program. 2006. Klamath River Blue-Green Algae Bloom Report. By Ken Fetcho, YTEP, Klamath, CA. 19 p.


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Appendix 1

Table 1. Responses to specific components of the Draft Workplan (NCRWQCB). Table derived from NCRWQWCB (2007) with added column for response.

Draft Klamath River Nutrient, Dissolved Oxygen, and Temperature TMDL

Implementation Plan Workplan Outline for CA

Topic Impair-ment Interested Parties Components Tribal Response

Interstate Water Quality

Temperature Nutrients Dissolved Oxygen

State of Oregon Regional Board

USEPA 9 and 10 Klamath Tribes

SWRCB

• Work with ODEQ to develop MOU to ensure that TMDL loading capacity and load allocations will lead to delivery of water across the OR/CA boundary that meets CA water quality objectives.

• Work with Oregon agencies to monitor effectiveness of MOU measures and implementation.

• Work with EPA 9 and 10 to coordinate implementation including the Lower Lost River Action Plan.

• ODEQ MOU needs to require specific steps to remediate acute water quality problems in Keno Reach, Lost River, and Upper Klamath Lake and specify monitoring requirements and a time line for meeting WQ standards.

• Need full funding for Hatfield Working Group, including science panel monitoring priorities.

• Draft Lower Lost River TMDL is anadequate. Needs to be remedied by: 1) restoring ecosystem function by restorating riparian wetlands, channel sinuousity, increasing wetland/lake size by flooding more of Tule and Lower Klamath Lakes, and 2) Use of constructed wetlands to treat Straits Drain effluent.

Point Source Discharges

Nutrients Dissolved Oxygen

Iron Gate Hatchery Tule Lake WWTP

Oregon Point Sources Oregon DEQ

• If appropriate, assure numeric effluent limits are incorporated into the NPDES permits to comply with TMDL implementation.

• Investigate Oregon Point Sources permits to incorporate needed effluent reductions into the MOU with ODEQ or appropriate agency.

• Should the Straits Drain be treated as a point source?


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PacifiCorp Relicensing


PacifiCorp SWRCB

Regional Board ODEQ Tribes BOR

NOAA

• Work with SWRCB, ODEQ and other agencies to ensure that the 401 certification and relicensing conditions for the PacifiCorp hydro facilities are consistent with TMDL load allocations.

• Develop monitoring plan for implementation measures.

• Explore dams’ influence on algae blooms and fish disease.

• Incorporate flow objective in Pacificorp license.

• 401 consistency is imperative,but there is no reason to believe that KHP impacts to water quality can be fully mitigated.

• If clear links to incidence of fish disease and toxic algae blooms are shown and problems cannot be remedied by other than dam removal, the TMDL should so state.

• Monitoring plan for implementation related to KHP should include both with and without dam contingencies.

• Flows are set by BOR, not PacifiCorp.

Range and Riparian Land Management


USFS BLM RCDs

Parties responsible for grazing activities Regional Board

• Grazing, Riparian, and Water Management Plan(s) on an as-needed, site-specific basis.

• Develop MOUs with USFS and BLM. • Develop/implement rangeland and land

stewardship measures that are TMDL compliant

• (in general, actions can be similar to Shasta).

• Direct impact to the mainstem Klamath from livestock grazing is localized (e.g. just above Horse Creek and PacifiCorp’s Ranch between Copco and Stateline).

• Stock water withdrawal on Middle Klamath tributaries could be major issue due to refugia or access for fall chinook.

• Riparian easements should be recommended for sensitive private lands.

Flow (timing)


USBOR (DWR??)

Water Rights Holders Irrigators

Stakeholders Dam Owners/Operators

• Explore methods to increase cold water flows for the benefit of Klamath River fisheries including impacts on fish disease and toxic algae blooms.

• Protect and restore Middle Klamath watersheds to maintain healthy sediment regime and riparian conditions to protect refugia.

• Remove dams to allow access to spring areas upstream of Iron Gate and Copco dams.


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• Ensure NMFS Biological Opinion flow RPA that BOR will implement is consistent with TMDL load allocations.

• Hardy Phase II provides “best science” basis for flow and the river should never be run lower than 1000 cfs under any circumstance.

• Incorporate Klamath Water Banking program into TMDL where applicable.

• Marginal lands need to be retired through purchase or easements, not subsidized on an annual basis.

• Flood lease lands to restore Tule Lake and Lower Klamath Lake: Increase storage, >WQ

SWRCB Water Rights Regional Board

• Work with State Division of Water Rights to establish a flow objective that addresses thermal refugia protection, fish disease, and algae blooms.

• Need to prevent future flow depletion of MK tribs, but solution to disease, algae blooms and refugia access may require KHP removal.


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Timber

Harvest on Private Lands

Temperature

Private Parties Conducting Timber Harvest Activities Regional Board

CDF Tribes

• Waste discharge requirements -general or specific, and waivers.

• Explore how existing permitting and enforcement programs including Timber Harvest Plan review process (CDF) can be made consistent with TMDL

• Habitat Conservation Plan coordination. • Explore ways to close gaps between federal

and private timber management and water quality protections.

• Explore ways to bring road density and maintenance to a level consistent with TMDL protection of thermal refugia and compliant with sediment prohibitions.

• Incorporate Stream and Wetlands policies into THP process.

• Explore ways that THP process can be more protective of and enhance thermal refugia and riparian function.

• Getting recognition of private timberland issues in TMDL development is very positive (limits to harvest rates, protection of riparian, limits to road density)

• Getting explicit language and action on these thorny issues in the final TMDL may be problematic.

• Should consider recommending easements or acquisitions of highly erodible or otherwise sensitive lands.

• Enhanced stream and wetland protection is laudible, but cumulative watershed effects can cause major riparian damage and loss of stream habitat diversity.

• Needs to specifically identify hydrological alteration due to timber harvest affect water quality, particularly in watersheds with high amount of area in transient snow zone.

Timber Harvest on

Public Lands Temperature

USFS BLM

Regional Board Tribes

• Continue cooperatively implementing the joint Management Agency Agreement (MAA) between SWRCB and the USFS (1981).

• Develop MOUs with USFS and BLM that address road maintenance and road density in addition to timber harvest BMPs that protect thermal refugia and riparian fxn.

• Incorporate future Stream and Wetlands Policy into MOUs.

• Lower Scott River, Walker Creek and Elk Creek are examples of where 1981 MAA has broken down and channel scour in January 1997 flood has caused loss or degradation of refugia.

• Need more management that is forest health driven and restores diverse stand age and hydrologic function.

• KNF needs to reduce its road network by 2/3 to make annual maintainance feasible.


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Irrigated Agriculture

Temperature Dissolved Oxygen Nutrients

Irrigation Districts RCDs DEQ BOR BLM

Tule and Lower Lake Wildlife Refuges

NRCS Private landowners US EPA 9 and 10

• Encourage development and implementation of water conservation practices that improve water quality and increase cold water flows.

• Incorporate Rapid Subbasin Assessments developed by NRCS into conservation strategy for irrigated ag.

• Explore ways wetlands can be used to decrease nutrient concentrations

• Integrate Lower Lost River TMDL Action Plan into Klamath TMDL.

• Explore funding options for conservation activities on irrigated ag land. (funding)

• Explore how ag waivers fit into implementation strategy.

• Need to recommend to SWRCB that no additional permits be issued in MK tribs unless offsetting conservation measures are implemented.

• Address riparian cultivation and diking of mainstem Klamath along the Keno Reservoir.

• Need easements for expansion of riparian for water filtration function

• Levee setbacks needed to improve filtration capacity and stop non-point source pollution, especially if Keno Dam stays.

• Expansion of wetlands and riparian areas on Lost River, Tule Lake and Lower Klamath Lake would increase nutrient stripping capacity and improve Straits Drain water quality problems. It would also have major benefits for suckers, which are also a designated beneficial use.

Fish Disease Temperature Nutrients

Pacificorp DEQ

NRCS RCDs/CRMP

Regional Board Tribes

USFWS BOR

NOAA

• Inhibit establishment of cladophora beds that provide habitat for intermediate host

• Connect flows with spread and control of disease

• Work with Pacificorp, BOR and NOAA to address factors affecting fish disease.

• Incorporate effects on fish disease into Klamath flow objective.

• Assumes connection between scour below Iron Gate and habitat for Manayunkia, but need further data to confirm.

• It is likely that lack of flushing flows in spring during years of succcessive drought contributes to fine sediment built up and reduces frequency of scour of algae beds.

• Requires re-establishing free-flowing river, access to refugia, and disbursement of spawners, not increasing flow from dams.

• Reducing the amount of organic matter in the river (e.g. by reducing pollution from upstream agriculture) should also reduce fish disease.


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Algae Blooms

Temperature Dissolved Oxygen Nutrients

Pacificorp DEQ

NRCS RCDs/CRMP

Regional Board Tribes BOR

NOAA

• Work with Pacificorp, BOR and NOAA to address factors affecting algal blooms

• Incorporate effects on algal blooms into Klamath flow objective.

• Explore how pulse or flushing flows contribute to controlling algal proliferation.

• Include WHO, SWRCB water quality standards as trigger for health advisories and as an implementation goal.

• Factors affecting algae blooms are Upper Klamath Lake limnology, nutrient contributions from agriculture and biological activity in reservoirs themselves. Reducing nutrients would help, but removing reservoirs also needed.

• Flow changes cannot likely reduce algae and nutrient problems.

• Should differentiate between phytoplankton (free-flowing algae) and periphyton (attached algae), not just use generic term “algae blooms”, as different solutions for each may be required.

County/State Roads


CALTRANS Siskiyou, Trinity,

Humboldt and Modoc Counties

Regional Board

• Evaluate and modify if needed Caltrans statewide NPDES stormwater permit.

• Work with counties to ensure road maintenance and construction programs are consistent with TMDLs and grading ordinances are developed and enforced.

• The contruction of highway 96 triggered many landsides, but most have now stabilized. NCRWQCB should ensure that Caltrans continues with policy of not side-casting mterials into the river during road maintenance activities (i.e. clearing landslides).

• Mitigation money should be directed at Hwy 96 barrier modification (refugia access)

• Good to work with counties on roads (pro-active versus reactive to prevent failures).

Riparian Function General

Temperature Dissolved Oxygen

Parties Responsible for Vegetation that Shades

Water Bodies

Regional Water Board

• Preserve and restore streamside vegetation

providing shade to watercourses. • Regional Water Board to develop

mechanisms, e.g., Waste Discharge Requirements (general or specific) or waivers, for addressing shade-providing riparian vegetation.

• This is particularly important on tributaries that serve as refugia.

• Biggest threat to riparian function is debris torrents and channel scour.

• Need to include cumulative watershed effects prudent risk levels of disturbance for watershed (road densities, percent harvest, disturbance of unstable ground).


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Septic Tanks Nutrients Dissolved Oxygen

Counties River communities (e.g., Orleans, Happy Camp,

Seiad Valley)

• Ensure that septic systems are not contributing nutrient load to the river.

• Likely more important as human health measure, but still needed.

Technical Support,

Outreach and Funding


NRCS UC Cooperative

Extension Regional Board

Tribes Local and Regional Watershed Groups

• Increase cooperation to provide technical support, education, and outreach.

• Work cooperatively with the NRCS and UCCE on technical support, educational and outreach efforts.

• Ensure various funding sources give priority to TMDL implementation projects.

• Funding sources: Prop 40, 50, 319(h), EQIP, DFG, NRCS, Tribes.

• Need to make sure that NRCS is mindful that ground water and surface water connections may make pumps a bad investment, if flows for fish are the objective.

• Need open sharing of information of how and where NRCS restoration funds are applied.

• Make sure that monitoring components are in place to insure that funds spent in the name of fisheries and water quality improvement are working.

• Technical support objectives should include information and data sharing.

Coho Recovery


CDFG Regional Board

• Work with CDFG to integrate Coho Recovery Strategy into TMDL.

• ITP? Explore w/ CDFG feasibility (and necessity) of drafting-implementing an Incidental Take Permit for listed fish species.

• ITP drafts have substantial major flaws, which if not corrected, would make them counter-productive to TMDL objectives.

• Scott and Shasta ITP drafts do not reflect TMDL findings in those basins.


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Gold Mining Temperature CDFG

New 49ers Regional Board

• Ensure mining activities are protective of thermal refugia and riparian function.

• Ensure mining activities are compliant with TMDLs and management goals.

• Work with CDFG to update their mining permits to comply with TMDL.

• Protection of refugia from mining is an important issue.

• Also need to protect stream banks and prevent non-point source pollution.

• Most significant risk is cumulative watershed effects if price of gold continues to climb (will lead to more mining).

• USFS cannot turn down mining claims due to 1872 Mining Law, but can ask for mitigation.

Bank Stabilization


Parties Responsible for Bank Stabilization

Activities Regional Board

• Encourage planting and restoration of flood control structures on/adjacent to stream banks

• Use existing authorities and regulatory tools (401 Water Quality Certification Program, etc.), to ensure proper bank stabilization and vegetation management.

• Issue of riparian function should also address wetland restoration and pulling back dikes along Keno Reservoir to expand wetlands and promote nutrient retention.

• We also recommend the use of conservation easements (e.g. to maintain/restore riparian buffers) as an inducement in additon to using a regulatory approach.


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Monitoring and Tracking


Regional Board NGOs

PacifiCorp USBOR Tribes CDF

Timber Harvest operations

USFS, BLM CDFG

• Coordinate with tribes and other agencies • Integrate TMDL results into ongoing

monitoring • Ensure TMDL implementation is resulting

in trend towards meeting load allocations and water quality objectives

• Fish disease – spore counts • Algae – WHO and SWRCB standards • Track MOU measures, RCD/CRMP efforts,

compliance with waivers and Stream and Wetlands Policy

• Include regular reporting to Regional Board • Monitor thermal refugia water quality and

functionality including fish counts.

• Specific monitoring strategies expected, including methods, locations and timing.

• Link to rates of pollution abatement, with expected timelines, and tiered actions, if water pollution abatement is not achieved.

• Monitoring should have two contingencies, with dam removal and without dam removal.

• TMDL Implementation Plan should include description of potential collaboration with Tribes and local NGOs for data acquisition.

• Restate need for mechanism for data sharing mechanism for adapative management (e.g. KRIS).

• Require data transparency (provision of raw data) from RCDs and CRMPs.

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