Permitting Study for the Proposed Dredging of Tequisquita

Slough, San Benito County, CA

Prepared for

Santa Cruz County Resource Conservation District 820 Bay Avenue, Suite 128, Capitola, CA 95010

sccrcd@sccrcd.org

Prepared by

Cameron Mumper University of California, Santa Cruz, Environmental Studies/Biology Undergraduate

cmumper@ucsc.edu

November 22, 2006

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Table of Contents_________________________________

Overview 1

Background Information 2 • Site Description 2

• Past and Present Tequisquita 3

• Groundwater Quality 4

• Hydrology 5

• Vegetation and Wildlife 5

Project Goals and Components 8

Permitting Triggers 10

• Endangered Species Act 10

California Red-Legged Frog 11

• Rivers and Harbors Act 14

• Clean Water Act 15

• California Environmental Quality Act 15

Permitting Agencies 18

• US Army Corps of Engineers 18

• US Fish and Wildlife Service and National Marine Fisheries Service 20

• California Department of Fish and Game 22

• San Benito County Public Works Department 25

• Regional Water Quality Control Board 26

Summary 28

Conclusion 29

References 30 Appendices 33

1

Overview____________________________________________

This paper was designed to give a detailed report of the agencies potentially

involved in a project proposed by the Santa Cruz County Resource Conservation

District (SCCRCD), entailing the one time dredging of 3,000 cubic yards of fill material

from Tequisquita Slough and the grading of approximately 0.25 miles of its banks.

Information for this paper was gathered by reviewing preexisting SCCRCD

documentation on Tequisquita Slough; arranging meetings with authorities from the

SCCRCD, California Farm Bureau, and Nature Conservancy; contacting

representatives of both federal and state agencies; researching agency policies online;

and conducting multiple field visits.

This paper begins with background information on Tequisquita Slough and a

description of the restoration activities proposed by the SCCRCD. This is followed by a

brief discourse on the federal and state legislation triggered by such activities, the

regulatory agencies responsible for enforcing restrictions established by the legislation,

and the permits required to comply with these restrictions. Included in this discussion

are several agency responses/recommendations to an application submitted by Dale

Rosskamp, San Benito County Public Works Department, in 2001 requesting the

issuance of a Mitigated Negative Declaration for the project. The paper ends with a

summation of the permits required for the proposed project, and the current gaps in

information responsible for withholding the issuance of such permits.

San Joaquin kit fox (Vulpes macrotis mutica)

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Background Information_______________________________

Site Description:

The Tequisquita Slough project site is located 1.7 miles west of the intersection

of Shore road and San Felipe road in Hollister, CA, resting within the 100-year

floodplain of the Pajaro River. The Pajaro River is the largest stream between San

Francisco Bay and the

Salinas River watersheds,

and is responsible for

draining more than 1,300

square miles of land,

including portions of Santa

Cruz, Santa Clara, San

Benito, and Monterey

Counties (Figure 2).

The slough receives inputs

from the western slope of

the Diablo Range, including Arroyo Dos Picachos, Arroyo de las Viboras, and Santa

Ana Creek. Pacheco Creek joins the slough just before it drains into San Felipe

Lake approximately 2.8 miles downstream of Shore Road. San Felipe Lake borders

both San Benito and Santa Clara County, and has a total catchment area of over

280 square miles (USDA, 2003). Current land use surrounding the slough includes

row crop agriculture, cattle grazing, and hay fields.

Past and Present Tequisquita:

Figure 1 A remotely sensed image of Tequisquita Slough’s location. The blue line indicates the slough’s current path, while the green line indicates its natural path.

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During the 1950’s, the last reach of Tequisquita Slough was realigned and

channelized by a nearby landowner to drain into Pacheco Creek at a 90o angle. The

slough’s natural channel was filled in, providing the landowner with new agricultural

prospects along the former riparian and wetland habitats (Figure 1). This

realignment led to a reduction in water velocity, gradual sediment deposition at the

angle of incidence, and the ponding of water within the slough (USDA, 2003). In the

1970’s, high velocity storm waters from Pacheco Creek deposited a great deal of

sediment into the realigned channel of Tequisquita Slough. This sediment

deposition blocked the engineered mouth of the slough, and consequently, flows

began to return to their natural path. Since the fill had not been removed from the

original channel, the water column remained shallow despite the continuation of

undiminished flows, and agricultural lands surrounding the slough became

progressively inundated by annual

floodwaters. Each year floodwater

advances further onto adjacent

agricultural lands and has created

persistent pools of standing water in

some areas (Figure 3). Currently,

the natural channel within the

project site is an estimated

21m wide and 1m deep.

Figure 2 The extent of the Pajaro River watershed and the respective counties that lie within its boundaries.

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According to Mary Ellen

Dick, Water Quality

Coordinator of the Central

Coast Agricultural Water

Quality Coalition, the

majority of landowners

affected by the inundation

wish the channel to be

returned to a depth

sufficient to lower the local groundwater table, attain an economic return on their

land, reduce flooding frequency and extent, renew steelhead passage upstream,

and enhance surrounding wildlife habitat. Inasmuch, landowners are willing to

acquiesce farmland for designation as wildlife habitat (Pers. comm., Jan 21, 2006).

Groundwater Quality:

Tequisquita Slough and San Felipe Lake have elevated levels of total dissolved

solids (TDS) attributed to excessive amounts of boron, chloride, sodium, and sulfate

latent within soils. Fertilizers and pesticides used for agricultural practices and

nearby septic tanks have also contributed to elevated TDS levels. Due to poor

groundwater quality resulting from elevated TDS levels and overdraft of the region’s

aquifer, the county began importing high quality surface water from the San Luis

Reservoir in the early 1980’s. As a result, groundwater levels have increased in the

Tequisquita Slough and San Felipe Lake region (USDA, 2003). Although the rising

Figure 3 Digital picture taken on April 5, 2006 of a marsh along the banks of Tequisquita Slough.

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groundwater table is not seen as a consequence of Tequisquita Slough’s

realignment, it represents an important consideration of the project site.

Hydrology:

Hydrology is possibly the most important feature of aquatic systems. Tequisquita

Slough rests in Pacheco River region of the extensive Pajaro River watershed. The

watershed is divided into the Corralitos, Uvas/Llagas, Pacheco, and San Benito river

regions, and is responsible for draining approximately 1,300 square miles of land,

covering portions of Santa Cruz, Santa Clara, San Benito, and Monterey counties.

Tequisquita Slough is encompassed within the river’s 100-year floodplain, but can

flood as frequently as every 10 years (USDA, 2003).

Vegetation and Wildlife:

Freshwater marsh and riparian vegetation line the banks of Tequisquita Slough,

and are typified by dense stands of Scirpus spp. and Typha spp., canopied by Salix

spp. Due to adjacent agricultural activities, vegetation is confined primarily to the

banks of Tequisquita Slough. However, in recent years flooding of adjacent

farmlands has persisted on a near annual basis, causing the slow expansion of

riparian vegetation onto farmland in pursuit of standing water sources. Amongst the

vegetation, one is likely to encounter bullfrogs (Rana catesbeiana), mosquitofish

(Gambusia affinis), pied-billed grebe (Podilymbus podiceps), bittern (Botaurus

lentiginosus), great blue heron (Ardea herodias), great egret (Ardea alba), mallard

(Anas platyrhynchos), sora (Porzana carolina) and the common moorhen (Gallinula

chloropus) (Bryan Mori, 2000). Although no site specific evidence exists, the

propensity of sloughs and wetlands to act as refuge for migratory species may lead

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to an increase in species richness during migration seasons. If this is true, the

chance of rare species seeking refuge within the project site greatly increases.

A literature review prepared in 2000 by the Bryan Mori Biological Consulting

Service noted the presence of the federally listed California red-legged frog (Rana

aurora draytonii) at three sites within 5 miles of the proposed project site (Bryan

Mori, 2000). Although no California red-legged frog (CRF) surveying was

conducted, the consultant reported that the project site could act as suitable CRF

habitat. During surveillance, the consultant noted several other listed species in the

project site. These include the federally listed San Joaquin kit fox (Vulpes macrotis

mutica) and least Bell’s vireo (Vireo bellii pusillus); the California species of concern

Western pond turtle (Clemmys mamorata), burrowing owl (Athene cunicularia), and

the tri-colored blackbird (Agelaius tricolor); and the candidate California tiger

salamander (Ambystoma californiense) (Bryan Mori, 2003). There currently exist no

data on the population size or distribution of the species listed above, including the

CRF, despite their significance in the project’s outcome.

A surprising discovery was made by John Smith, Department of Biological

Sciences at San Jose State University, at San Felipe Lake in 2005. San Felipe Lake

is located in the Pajaro River watershed and receives inputs from Pacheco Creek

and Tequisquita Slough. During routine fish sampling in late June, two adult

Chinook salmon (Oncorhynchus tshawytscha) were identified in the lake (Smith,

2005). Smith believed both had apparently recently migrated from the ocean, even

though the timing was too early for freshwater entrance by fall-run Chinook (Moyle

2002). Interestingly, multiple studies have shown the temperature range and low

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oxygen content of the watershed to exceed the tolerance of salmon, and past

studies have not reported Chinook in the Pajaro River watershed (Smith 1982). This

suggests that the sighting of the convict salmon was a random occurrence and that

salmon do not typically inhabit San Felipe Lake or any of its tributaries.

Nevertheless, the Pajaro River watershed contains several regions of steelhead

trout (Oncorhynchus mykiss) habitat. Within the Pacheco Creek region, Arroyo de

los Picachos provides some of the best remaining steelhead spawning and rearing

habitat (Smith, 2005). According to Arianne Rettinger, SCCRCD Pajaro Watershed

Coordinator, NOAA officials believe this region would be greatly enhanced if

Tequisquita slough were opened up to allow passage of steelhead into Arroyo de los

Picachos (Pers. comm., Nov 10, 2006).

California red-legged frog (Rana aurora draytonii)

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Project Goals and Components_________________________

The main goals of the Tequisquita Slough project are to reduce flooding

frequency and extent on adjacent farmland, renew steelhead passage upstream, and

enhance surrounding wildlife habitat. To accomplish these goals, the SCCRCD has

proposed a project entailing the reconfiguration of a 0.25 mile portion of Tequisquita

Slough’s channel to more accurately represent its historical conditions.

One proposed design solution involves the deepening of the existing channel by

removing approximately 3,000 cubic yards of fill from the channel and grading

approximately 0.25 miles of its banks. Deepening of the channel will increase water

velocity, reduce sediment deposition, arrest the expansion of water onto surrounding

agricultural lands, and provide steelhead passage into Arroyo de los Picachos. Grading

along the banks will provide a shallow habitat for many amphibious species, including

CRFs and Tiger Salamanders, and possibly steelhead. Native hydrophilic vegetation

will be planted along the banks to offset construction activities and provide habitat for

existing species.

Alongside agricultural lands severely impacted by flood waters, the SCCRCD

proposes to create wetlands that will act as flood planes during periods of high flows

and promote the persistence of native wildlife. Riparian buffer zones would be created

between the wetlands and agricultural fields to reduce flooding and intercept runoff

pollutants from surrounding agricultural practices. Only native hydrophilic vegetation

would be planted to establish a low maintenance, sustainable ecosystem requiring

minimal future maintenance. A brief discussion of a potential design solution for

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wetland creation can be found in Appendix B. At this point, more detailed information is

required because it is unclear whether local hydrology will support a created wetland.

Great blue heron (Ardea herodias)

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Permitting Triggers____________________________________

The proposed activities are likely to trigger both federal and state legislation.

Potential impacts to threatened, endangered, and/or sensitive species that inhabit the

project site fall under the jurisdiction of the Endangered Species Act (ESA). The

proposed grading and dredging activities have the potential to discharge materials into

U.S. waters, and therefore are regulated by the Rivers and Harbors Act of 1899 (RHA)

and the Clean Water Act (CWA). All discretionary activities proposed to be conducted

in California must comply with the California Environmental Quality Act (CEQA) unless

otherwise exempt.

Endangered Species Act

The purpose of the ESA is to protect and recover imperiled species and the

ecosystems upon which they depend (USFWS, 2006). Enacted by Congress in

1973, the ESA represents the only federal protection for threatened and endangered

species nationwide. ESA Section 7 requires federal agencies to consult with the

U.S. Fish and Wildlife Service and the National Marine Fisheries Service to ensure

actions they authorize, fund, or carry out will not jeopardize protected species. If a

project is likely to involve the “take” of a listed species, the lead agency may apply

for an incidental take permit through ESA Section 10 provided they have developed

a Habitat Conservation Plan (HCP). “Take” is defined as, “harass, harm, pursue,

hunt, shoot, wound, kill, trap, capture, or collect or attempt to engage in any such

conduct.” An HCP is a mandatory component of an incidental take application that

outlines the potential impacts to listed species within the project site, the steps to be

taken to minimize and mitigate those impacts and ensure there is no net negative

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effect on the population of the species, and the funding available to implement those

steps. The lead agency may apply for an incidental take permit once the HCP is

approved by the U.S. Fish and Wildlife Service or the National Marine Fisheries

Service (USFWS, 2006).

California Red-Legged Frog

The California red-legged frog (CRF) is a federally endangered species

believed to inhabit the project site. In 2000, the Bryan Mori Biological Consulting

Service compiled a CRF site assessment for Tequisquita Slough. The report

indicated the potential for the project site to act as suitable CRF habitat, given the

vegetation present and the slough’s close proximity to three sites with

documented CRF sightings. Since the SCCRCD does not have the resources to

complete an HCP, it is essential to determine whether CRFs currently inhabit the

slough, and the extent of their distribution and population size. It is equally

important to determine whether any physical alterations to the channel will

endanger any resident CRFs.

• Ecology:

Typically, all CRF life history stages occur near breeding sites, which are

known to include coastal lagoons, marshes, springs, permanent and semi-

permanent natural ponds, ponded and backwater portions of streams, as well as

artificial impoundments such as stock ponds, irrigation ponds, and siltation

ponds. Eggs are usually attached to emergent vegetation, such as cattail (Typha

spp.) and bulrush (Scirpus spp.), in ponds or backwater pools in creeks.

However, they have been found in areas completely denuded of vegetation.

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CRF populations are densest in creeks and ponds characterized by thick woody

riparian vegetation, especially willows (Salix spp.) (Hayes and Jennings, 1988).

• Current Data:

In July of 2000, the Bryan Mori Biological Consulting Service prepared a

California red-legged frog (CRF) site assessment for the San Benito County

Public Works Office. The assessment entailed an on-site field reconnaissance,

literature review, access of the California Natural Diversity Data Base (CNDDB),

as well as, discourse with other consultants to document CRF occurrences within

a 5-mile radius of the project site (Bryan Mori, 2000).

According to their literature research and consultation, there have been at

least three know CRF occurrences within 5 miles of the project site. These

include a 1990 sighting of 40 adults in a large pond approximately 1,056 feet

downstream of the project site; larvae in Pacheco Creek, 3.4 miles east of the

project site at HWY 156 in 1991; and a 1998 sighting of larvae and adults in an

agricultural drainage channel in 1998, approximately 3.6 miles west of the project

site (Bryan Mori, 2000).

The consultant concluded that the project site, “likely provides potential

habitat for CRF,” given the CNDDBs records of 40 adults downstream from the

project site. They also asserted that the channel could be used for CRF breeding

while the marsh and riparian habitat along the channel provides potential cover

for adults and juveniles. However, they maintained the overall habitat quality

may be less than optimal for CRF due to the presence of bullfrogs, which have

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been known to prey on adults and juveniles, and mosquitofish, which consume

eggs and prey on recently hatched CRF larvae (Bryan Mori, 2000).

• Gap Analysis:

Despite the research and field visits made by the Bryan Mori Biological

Consulting Service, they made no attempt at nocturnal or diurnal visual, eye-

shine, or auditory surveillance for CRF. The majority of their efforts were

directed toward inferences of existence based on preferential habitat and

proximity of sightings. Nocturnal surveys serve the purpose of identifying and

locating adult and metamorphosed frogs. Diurnal surveys during the breeding

season help identify larvae, metamorphs, and egg masses, while diurnal surveys

during the non-breeding season help identify metamorphosing sub-adults, and

non-breeding adults. Auditory surveys are usually conducted just before visual

or eye-shine surveys to document the presence of calling frogs before disturbing

their habitat. Although a calling male can aid in locating the individual frog,

counting calls is not a reliable method for determining population size. Rather,

the counting of egg masses gives a much more reliable method of determining

the number of breeding adults (USFWS, 2005). Therefore, combining adult frog

surveys at night with egg mass surveys during the day provides a more

comprehensive account of CRF population size at a given site.

Given the close proximity of CRF sightings, and the slough’s ability to act as

suitable habitat for CRF, surveillance is a necessary component that can ensure

the SCCRCDs compliance with Section 7 of the ESA by providing existence data

of CRFs in the project site. Considering the U.S. Fish and Wildlife Service

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updated its CRF surveying protocol in August, 2005, the sightings presented by

the Bryan Mori Consulting Service may not be upheld by ESA requirements

given the most recent account dates back to 1998 (USFWS, 2005).

Furthermore, updated surveying protocol from the California Department of Fish

and Game states that any reports of CRFs on a site within the past five years

establishes the species as present with no further survey work needed provided

that no significant habitat alterations have occurred since the surveillance

(CDFG, 2005c). The consultant’s CRF assessment falls outside this five year

window. The SCCRCD will be unable to continue the project if required to obtain

an incidental take permit and create a HCP, and therefore requires data on the

existence and distribution of CRF and other listed species within the project site.

A brief summary of my personal experience with CRF surveying and field visits to

Tequisquita Slough can be found in Appendix C.

Rivers and Harbors Act

The RHA was established in 1899 with the intent to regulate any construction

projects that would obstruct the path of U.S. navigable waters. RHA Section 10

prohibits any construction, excavation, or deposition activities that could potentially

alter the course, location, condition, or capacity of U.S. waters without first obtaining

a permit. Such activities include the construction of piers, wharfs, breakwaters,

bulkheads, jetties, weirs, and transmission lines, as well as, dredging, excavation,

and filling, of U.S. navigable waters (FEMA, 2006).

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Clean Water Act

The CWA was established to restore and protect the quality of the nation’s

surface waters by regulating the discharge of pollutants into navigable waters.

Surface waters include rivers, lakes, intermittent streams, and wetlands. Section

404 of the CWA establishes a federal program aimed at regulating the discharge of

dredged or fill material into U.S. waters and wetlands. The program was established

to ensure that no dredge or fill material will be released into U.S. waters if a practical

alternative exists that is less damaging to the environment, or if the nation’s waters

would be significantly degraded as a result of the discharge (EPA, 2006a). Before

dredged or fill material may be released into U.S. waters, the party responsible for

the activities must either attain a discharge permit or file for an exemption from the

U.S. Army Corps of Engineers. Filling and grading, mechanized clearing and

ditching, or other excavation activities constitute activities regulated by the program

(EPA, 2006a). In addition, CWA Section 401 requires any applicant requesting a

federal permit to comply with state water quality standards by obtaining State Water

Quality Certification. In California, Regional Water Quality Control Boards maintain

Water Quality Control Plans for each major hydrologic basin. It should be noted that

certain dredging activities may require the applicant to enter into a Streambed

Alteration Agreement with the California Department of Fish and Game depending

on the severity of impact to protected species (SWRCB, 2003).

California Environmental Quality Act

The main objectives of CEQA are to disclose to decision makers and the public

the significant environmental impacts likely to result from a project’s activities, and to

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require agencies involved in such activities to avoid or reduce these impacts by

implementing feasible alternatives or mitigation measures. CEQA applies to all

discretionary activities proposed to be carried out or approved by California state,

regional, county, and local agencies, unless a statutory exemption applies. The

CEQA process has three fundamental phases: 1) conducting a preliminary

environmental review 2) preparation of an Initial Study (IS) 3) and preparation of

either a Negative Declaration (ND) or an Environmental Impact Report (EIR). CEQA

documentation is generally included in a permit application to convey the project’s

potential environmental impacts, and any mitigation measures adopted to reduce

such impacts to a non-significant level.

In 2004, a new categorical exemption (CEQA Guidelines Section 15333) was

developed for small habitat restoration projects on 5 acres of land or less. Section

15333 has three limitations: 1) The project must involve no significant adverse

impact on endangered, rare, or threatened species or their habitat 2) The project

must not disturb or release any hazardous materials at or around the project site 3)

The project must not result in impacts that are significant when viewed in connection

with the effects of past projects, the effects of other current projects, and the effects

of probable future projects. Examples of small restoration projects include:

revegetation with native plants; wetland restoration to improve waterfowl conditions;

stream or bank restoration to benefit native fish or amphibian habitat; stream or bank

stabilization with native vegetation for the purpose of eliminating erosion and

sedimentation; and culvert replacement for the purpose of improving habitat and

reducing sedimentation (CERES, 2005).

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Western pond turtle (Clemmys mamorata)

The major challenge in using this exemption is that it is new and there is little, if

any, precedent or specific guidance for its application. If this categorical exemption

is not applicable, project proponents will need to complete an Initial Study (IS) and

circulate it to all responsible and trustee agencies before applying for any permits.

The findings of the IS will determine whether an Environmental Impact Report (EIR)

or Negative Declaration (ND) should be prepared by the lead agency. In general, if

the project will result in potentially significant environmental impacts that cannot be

mitigated by changes in the project design or implementation, the agency may be

required to prepare a draft EIR. If there are no potential significant impacts, or the

impacts can be reduced to a less than significant level by amending the project

design or implementation, the lead agency will be required to produce a ND or a

Mitigated Negative Declaration (MND) in order to comply with CEQA. The SCCRCD

should consult with the various agencies to determine if the project has the

possibility of exemption from CEQA (Martin et al., 2004).

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Permitting Agencies___________________________________

There are several potential key permitting agencies involved in the project. They

include the United States Army Corps of Engineers (USACE), United States Fish and

Wildlife Service (USFWS), National Marine Fisheries Service (NMFS), California

Department of Fish and Game (CDFG), San Benito County Public Works, and the

Central Coast Regional Water Quality Control Board (RWQCB).

• US Army Corps of Engineers:

Projects discharging dredged or fill material into navigable waters of the U.S.,

including wetlands, are subject to USACE jurisdiction. USACE enforces Section 404

of the Clean Water Act (CWA) and Section 10 of the Rivers and Harbors Act (RHA).

CWA Section 404 requires authorization prior to discharging dredged or fill material

into waters of the U.S., including wetlands. Such discharges may result from

navigational dredging, flood control channelization, levee construction, channel

clearing, fill of wetlands for development, or other activities. These projects involve

the removal or placement of soil, sediment, and other materials in or near water

bodies and require Corps permits under CWA Section 404 (CERES, 2003). RHA

Section 10 prohibits the unauthorized obstruction or alteration of any navigable

waters of the U.S without a permit from USACE.

USACE issues individual or general permits under Section 404 and Section 10.

Individual permits are required for a project resulting in potentially significant

environmental impacts, whereas general permits certify projects causing minimal

environmental impacts. General permits are issued by USACE on a nationwide,

regional, or statewide basis to streamline the Section 404 process for activities

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having minimal environmental impacts (EPA, 2006a). A Nationwide Permit (NWP) is

a general permit that authorizes a category of activities throughout the nation, and is

valid only if the conditions applicable to the permit are upheld. If the conditions

cannot be upheld, a regional or individual permit will be required (Martin et al.,

2004).

According to Bob Smith, USACE San Francisco District, the specific activities of

the Tequisquita Slough Project will likely be considered restoration activities under

the definitions of NWP 27 (Pers. comm., Mar 1, 2006). NWP 27 certifies the

restoration of former waters, and the enhancement of degraded tidal and non-tidal

wetlands and riparian areas1. Some of the permissible activities pertinent to the

project include: the removal of accumulated sediment; the enhancement, restoration,

or creation of riffle and pool stream structure; the placement of in-stream habitat

structure; modifications of the stream bed and/or banks to restore or create stream

meanders; the backfilling of artificial channels and drainage ditches; activities

needed to reestablish vegetation, including plowing or discing for seed bed

preparation, and the planting of appropriate wetland species; and mechanized

clearing to remove non-native invasive, exotic or nuisance vegetation (Federal

Register, 2002).

Most projects that qualify for a NWP will require CWA 401 certification from the

state to ensure compliance with state water quality standards. The Regional Water

Quality Control Board has exempted certain activities authorized by NWPs if they

1 See the form attached to the end of this paper for more detailed information on NWP 27

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are conducted in compliance with conditions specified in the certification (SWRCB,

2003).

Section 11(a) of NWP 27 expressly discloses that authorization will be withheld if

the project violates Section 7 of the ESA by jeopardizing the continued existence of

a threatened or endangered species. Inasmuch, non-federal permittees must notify

the District Engineer if any federally listed species or designated critical habitat might

be directly impacted by, or is in the vicinity of, the project site (USACE, 2002). This

poses a concern given the documented sightings of CRF within 5 miles of the project

site, as well as, the numerous other sensitive species identified in the region.

Furthermore, in August of 2005 the USFWS updated their CRF surveying protocol2.

Given that the previous assessment was conducted using the now obsolete

guidelines from 1995, it is likely that the FWS will require further surveillance that

adheres to the new guidelines.

• US Fish and Wildlife Service and National Marine Fisheries Service:

The USFWS and NMFS jointly administer the provisions of the ESA. USFWS

has jurisdiction over all non-marine species, while NMFS has jurisdiction over

federally listed anadromous fish species (USFWS, 2004). If a project’s activities are

likely to result in “take” of a federally listed species, USFWS and/or NMFS in

consultation with the lead agency, may issue an incidental take permit pursuant to

ESA Section 10. For example, if the USACE determined that issuance of a 404

permit will likely impact a listed species, they must initiate Section 7 consultation with

USFWS and/or NMFS (Martin et al., 2004).

2 Updated protocol can be found at http://www.fws.gov/sacramento/es/documents/crf_survey_guidance_aug2005

21

Consultation may be either informal or formal depending on the potential impacts

of the project. NMFS and USFWS conduct informal consultations when the impacts

of a proposed project are discountable, insignificant, or completely beneficial to the

listed species with no incidental take occurring (Martin et al., 2004). The

determination to conduct an informal consultation requires the SCCRCD to supply

USACE with sufficient information on the project activities and the species of

concern. For example, if the project is located in or near suitable habitat for the

CRF, or in a stream that supports migration, spawning, or rearing of salmonids, and

the applicant shows that during construction the area will be avoided, it is possible

that consultation will proceed informally with USFWS and/or NMFS. On the other

hand, if project activities occur in areas characterized as suitable habitat for the CRF

and the absence of individuals could not be proven via presence/absence surveys,

or if salmonids have to be moved from the project site area during dewatering

activities, such project activities will likely result in “take” and trigger a formal

consultation with USFWS and/or NMFS that could last 90-150 days (Matrin et al.,

2004). According to Dave Pereksta, USFWS Ventura Office, the FWS would

informally consult with USACE over Section 7 compliance since the project will likely

fall under NWP 27 (Pers. comm., Mar 1, 2006).

It should be noted that some projects fall under a Programmatic Consultation/

Programmatic Biological Opinion (PBO), which enable an applicant to avoid time

intensive formal consultations even if the project at hand is likely to significantly

impact threatened or endangered species. A Programmatic Biological Assessment

is prepared that outlines potential impacts of the project and potential mitigation

22

activities. If the USFWS and/or NMFS concur with the conditions established by the

Biological Assessment the project is appended to the PBO. The PBO mechanism

likely to include the proposed project is the RCD/NRCS County-wide Permit

Coordination Program for projects funded through the CDFG’s Fisheries Restoration

Program. Under this program, permitting agencies enter into programmatic

agreements with the National Resource Conservation Service (NRCS) and

SCCRCD that cover 15 specific, standardized conservation practices (Martin et al.,

2004). According to Arianne Rettinger, SCCRCD Pajaro Watershed Coordinator,

the permit coordination program currently applies only to Santa Cruz County and is

not expected to extend through San Benito County until 2008 (Pers. comm., Oct 23,

2006).

• California Department of Fish and Game:

The Department of Fish and Game is responsible for conserving, protecting, and

managing California's fish, wildlife, and native plant resources. Fish and Game

Code section 1602 requires any person, state, local governmental agency, or public

utility to notify the regional department before beginning an activity with the potential

to substantially modify the natural flow, bed, channel, or bank of any river, stream, or

lake containing fish or wildlife resources, or habitat from which these resources

derive benefit (CDFG, 2005a). Section 1602 applies to all perennial, intermittent,

and ephemeral rivers, streams, and lakes in the state. Depending on the intensity of

proposed activities, the lead agency may be required to enter into a Streambed

Alteration Agreement (SAA). If an agreement is required, the Department will

conduct an onsite inspection and submit a draft agreement to the applicant,

23

including measures to protect fish and wildlife resources during the project’s

implementation (CDFG, 2005b). If the draft agreement terms are acceptable, the

applicant must sign the agreement and submit it to the Department. If there is a

disagreement with any terms in the draft agreement, the applicant must specify the

measures that are not acceptable. In this case, the CDFG and the applicant will

meet to resolve the conflict and finalize the agreement (CDFG, 2005b).

CDFG must comply with CEQA before issuing a final SAA. Issuance of a final

agreement occurs after the CDFG receives a draft agreement from the applicant and

signs it. If the Department receives a signed draft before the lead agency has fully

complied with CEQA, it must wait for the lead agency to fully comply with CEQA

before it may finalize the draft (CDFG, 2005b).

Any project that requires either CDFG permits or a discretionary permit triggering

CEQA will be required to address potential impacts to listed species. Most, if not all,

projects focused on fish passage and bank stabilization will require a SAA (Martin et

al., 2004). Since a goal of this project is to create steelhead passage, the lead

agency will be required to enter into an agreement with the CDFG. As of July 28,

2006, the CDFG revised its Streambed Alteration Notification FG2023 form3. The

more pressing concern, however, focuses on whether the project will require the

issuance of an incidental take permit. Section 2080 of the Fish and Game Code

prohibits "take" of any endangered or threatened species as mandated by the

California Endangered Species Act (CESA). Fish and Game Code section 2081

grants the CDFG power to issue incidental take permits for otherwise lawful activities

3 An update form can be found at http://www.dfg.ca.gov/1600/NotificationPackage. See the attachment at the end of this paper for more detailed information on the notification process.

24

(CDFG, 2006). Incidental take of fully protected species is prohibited unless the

project’s purpose is the recovery of that species. Notification is generally required

for any project that will take place in, or within, the vicinity of any river, stream, lake,

or their tributaries. This includes rivers and streams that flow through a bed or

channel with banks that support fish or other aquatic life, and watercourses that

have a surface or subsurface flow that support, or have supported, riparian

vegetation. As a general rule, it applies to any work done within the annual high-

water mark of a wash, stream, or lake that contains or once contained fish and

wildlife, or that supports or once supported riparian vegetation. In some cases, this

requirement may apply to any work undertaken within the 100-year floodplain of a

body of water or its tributaries, including intermittent streams and desert washes

(Martin et al., 2004). The lead agency is not required to obtain an incidental take

permit if the project is part of the management of a species or enhancement of the

species and its habitat. However, the Department is still required to complete a

Negative Declaration or an EIR (CDFG, 2006).

Consideration for CDFG certification will only commence once the gap in

biological data concerning endangered or threatened species within the Tequisquita

Slough project site is filled.

In May of 2001, the CDFG responded to the request for a MND received from

Dale Rosskamp, San Benito County Public Works Department. The following is a

list of comments by the CDFG:

1. “The proposed mitigation for capturing and relocating CRF away from the project site may be ineffective given their propensity to return to the area they were captured.”

25

2. “Aside from CRF, no discussion was made of other sensitive species in the project site that may be impacted by the project.”

3. “The extent of impact to riparian and wetland habitats needs to be clearly identified. For instance, if riparian vegetation removal extends beyond cutting cattails and tules to bring in equipment, these impacts may need mitigation.”

4. “A complete assessment of the impacts the project will have on the hydrology and water quality of the slough and San Felipe Lake should be addressed. This would include a discussion of how the streambed will be recontoured and a thorough analysis of the impacts that the resulting pulse of water will have on aquatic organisms once the sediment is removed.”

• San Benito County Public Works:

The San Benito County Public Works (SBCPW) department is responsible for

safeguarding public health, property, and general welfare by regulating grading,

drainage, and erosion control on private and public property. The Department

achieves these goals by requiring grading, erosion, and drainage control plans for

activities with the potential to cause water pollution and sedimentation in the

County’s water resources. Chapter 7A of the San Benito County Code establishes

the administrative procedures involved in the issuance of permits required for

grading activities (SBCPW, 2004). Given the project’s scope, Chris Herera of the

SBCPW believes a Chapter 7A grading permit will be required (Pers. Comm., Mar 3,

2006).

All grading permit applications are required to be accompanied by supporting

data consisting of a Soil Engineering Report and a Geologic Report, unless waived

by the County because information is available showing such data are not needed.

The Soil Engineering Report should include data regarding the nature, distribution,

and strength of existing soils, conclusions and recommendations for grading

procedures, design criteria for corrective measures when necessary, and opinions or

recommendations covering adequacy of sites to be developed by the proposed

26

grading. The Geologic Report should include an adequate description of the

geology of the site, conclusions and recommendations regarding the effect of

geologic conditions on the proposed development, and opinions and

recommendations covering the adequacy of sites to be developed by the proposed

grading (SBCPW, 2004).

Geological studies should focus on the elevated TDS levels found in the project

site and the potential impact of their release on aquatic organisms. These studies

should include an estimate of the amount of sediment to be released and its

chemical composition. Sediment disposal plans should be included in the

application and reflect the findings of the geological studies. One proposed disposal

plan includes the tilling of the removed sediment into nearby farmlands, provided it

does not contain hazardous contaminants.

• Regional Water Quality Control Board:

Pursuant to Section 401 of the CWA, the RWQCB has the authority to issue,

waive, or deny certification to any proposed activity involving state water quality

standards. Certification is generally triggered by the potential for a project to

discharge material into a waterway. Examples of projects requiring 401 certification

include, grading activities, stream bank restoration, preparations for planting, and

construction of underground drainage facilities (Martin et al., 2004). It should be

noted that any project requiring federal certification must obtain certification through

the State’s Water Quality Certification Program (EPA, 2006). Therefore, in order for

the RWQCB to certify a project as 401 compliant, the project must have a completed

27

California tiger salamander (Ambystoma californiense)

404 authorization, fulfilled the CEQA Guidelines, and completed all other applicable

state or federal permits.

In June of 2001, the Central Coast RWQCB responded to the request for a MND

received from Dale Rosskamp, San Benito County Public Works Department. The

following is a list of comments by the RWQCB:

1. “The justification for the dredging should stress the cause of flooding, how dredging will alleviate the flooding, and how much flood protection will be accomplished by the dredging.”

2. “Research past dredging activities to determine if the project will require more than a single dredge.”

3. “If riparian restoration is used as mitigation for dredging activities by controlling floodwaters, the Negative Declaration should address the possibility that farmland will be taken out of production.”

4. “Address the biological impacts that could result from the lowering of the elevation of water in the slough, such as increased temperatures, decreased oxygen concentrations, increased predation, and remobilization of contaminants currently present in sediments. Impacts to the riparian corridor, such as drying of the soil, should also be considered.”

5. “Farmland located within the floodplain is expected to flood periodically. Cover crops and riparian corridor enhancement are preferred alternatives for protecting farmlands. These will require agreements with landowners.”

6. “Monitoring downstream of the dredging will be required to verify excessive turbidity does not occur. Permission must be given from landowners allowing sediment to be tilled into their land. Furthermore, the sediment composition must comply with regulations.”

7. “Comprehensive profiling of the slough’s streambed.”

28

Summary____________________________________________

Although relatively small in scale, the proposed Tequisquita Slough project

requires compliance with strict legislation upheld by several federal and state agencies.

At this point, the paucity of biological, hydrological, and geological data has stalemated

the project in the design phase because sufficient data are not available to guide the

project’s implementation. Nor are data available to design project alternatives and

mitigation measures, or designate a level of potential environmental impact. Without

such data, regulatory agencies will likely reject any application requesting project

certification. This was the case in 2001, when a proposed ND was denied on the

grounds of insufficient data. The agencies responses provide a good starting point for

regaining project momentum, as do the personal communications with representatives

from these agencies. It will be important for the SCCRCD to partner with regulatory

agencies in order to complete CEQA documentation and apply for the appropriate

permits. TNC is currently engaged in an extensive restoration project throughout the

Pajaro River watershed, and could aid in compiling data that satisfy the comments

made by the regulatory agencies.

Tri-colored blackbird (Agelaius tricolor)

29

Steelhead trout (Oncorhynchus mykiss)

Conclusion__________________________________________

At this point, data acquisition is the next step in the project. This will allow the

SCCRCD to begin designing project plans and determine what, if any, alternatives are

feasible. Nevertheless, representatives from the respective regulatory agencies listed

throughout this paper were able to give professional opinions on the permits required for

the project when given the information available. A flow chart outlining the likely

permitting path for the Tequisquita Slough project can be found in Appendix D. The

overall steps are outlined below:

1. Follow CEQA Guidelines and prepare an Initial Study with comprehensive biologic, hydrologic, and geologic analysis.

2. a) If CRF or any other endangered or threatened species is present, consult with USFWS, NMFS, and CDFG about aiding in the development of an HCP. b) If no endangered or threatened species are present, or the project’s impacts can be mitigated without the potential for incidental take, then apply for other permits listed below.

3. Apply to USACE for NWP 27. 4. Enter into Streambed Alteration Agreement with CDFG. 5. Submit Soil and Engineering Report and Geologic Report alongside

application for Section 7A Grading Permit from San Benito County Public Works department.

6. Apply for 401 certification from RWQCB.

30

References__________________________________________

Bryan Mori Biological Consulting Services. (2000). California Red-Legged From Site

Assessment: Tequisquita Slough, San Benito County. Report for the San Benito

County Public Works Offices. 7pp.

CDFG. (2005a). Lake and Streambed Alteration Program. Retrieved June 22, 2006

from http://www.dfg.ca.gov/1600

CDFG. (2005b). Lake and Streambed Alteration Program, Questions and Answers.

Retrieved October 20, 2006 from http://www.dfg.ca.gov/1600/qa.html

CDFG. (2005c). Revised Guidance on Site Assessments and Field Surveys for

California Red-legged frog. Retrieved May 15, 2006, from

www.dfg.ca.gov/hcpb/species/stds_gdl/amp_sg/CRF%20Survey%20Guidance%

20Aug2005_Final.pdf

CDFG. (2006). Environmental Review and Species Take Permits. Retrieved October

27, 2006 from http://www.dfg.ca.gov/hcpb/ceqacesa/cesa/incidental/cesa_

policy_law.shtml

CERES. (2003). Water Quality Certification for Discharges of Dredge and Fill Materials.

Retrieved May 25, 2006 from http://ceres.ca.gov/wetlands/permitting/401.html

CERES. (2005). 15333: Small Habitat Restoration Projects. Retrieved October 30, 2006

from http://ceres.ca.gov/topic/env_law/ceqa/guidelines/art19.html

EPA. (2006). Wetland Regulatory Authority. Retrieved June 22, 2006 from http://

www.epa.gov/owow/wetlands/pdf/reg_authority.pdf

EPA. (2006). Clean Water Act, Section 401 Certification. Retrieved June 22, 2006 from

http://www.epa.gov/OWOW/wetlands/regs/sec401.html

FEMA. (2006). Clean Water Act (CWA), 1948 As Amended 1966, 1972, Section 10

Rivers And Harbors Act (RHA), 1899. Retrieved October 30, 2006 from

http://www.fema.gov/plan/ehp/ehplaws/cwa.shtm

Figure 2. “Pajaro River Watershed County Boundaries”. Pajaro River Watershed Flood

Prevention Authority. Retrieved October 30, 2006 from

http://www.pajaroriverwatershed.org/pages/study.htm

31

Hayes, M.P., and M.R. Jennings. (1988). Habitat Correlates of Distribution of the

California Red-Legged Frog. Proceedings of the Symposium on the Management

of Amphibians, Reptiles, and Small Mammals in North America. United States

Department of Agriculture, Forest Service, General Technical Report (RM-166):

1-458.

Martin, N., K. Goodnight, and K. Christensen. (2004). IWRP Design and Permitting

Coordination Process Guidelines Manual. Report for Santa Cruz County.

Mitsch, J.W. and J.G. Gosselink. (2000). Wetlands (3rd ed.). New York: John Wiley and

Sons, Inc.

Moyle, P. B. 2002. Inland Fishes of California. University of California Press. 302 pp.

Ogawa, H., and J.W. Male. (1986). Simulating the Flood Migration Role of Wetlands.

Journal of Water Resource Planning and Management, 112: 114-128.

SBCPW. (2004). An Ordinance to Regulate Grading, Drainage, and Control Erosion in

San Benito County. Retrieved April 23, 2006 from http://www.san-benito.ca.us/

departments/dpw/grading_ordinance.htm

Smith, J. J. 1982. Fishes of the Pajaro River System, in Studies on the distribution and

ecology of stream fishes of the Sacramento-San Joaquin drainage system, CA.

P. B. Moyle (ed), University of California Publications in Zoology 115: 83-169.

Smith, J. J. (2005). Aquatic Ecology and Fisheries of San Felipe Lake. Report to the

PRWFPA Staff Working Group. 40pp.

SWRCB. (2003). 401 Questions and Answers. Retrieved November 3, 2006, from http://

www.swrcb.ca.gov/cwa401/docs/stateregulation_isolatedwaters.pdf

Federal Register. (2002). Issuance of Nationwide Permits. Retrieved May 13, 2006 from

http://www.usace.army.mil/cw/cecwo/reg/2002nwps.pdf

USACE. (2002). Nationwide Permit Summary. Retrieved May 13, 2006 from

www.spa.usace.army.mil/reg/NATIONWIDES-NEW/NW27-wetln.pdf

USDA. (2003). Tequisquita Slough Feasibility Study. Prepared by the Natural Resource

Conservation Service.

USFWS. (1994). Habitat Conservation Planning and Incidental Take Permitting

Handbook. Retrieved October 21, 2006 from

http://www.fws.gov/Endangered/hcp/hcpbook.html

32

USFWS. (2004). Endangered Species Related Laws, Regulations, Policies & Notices.

Retrieved May 21, 2006 from http://www.fws.gov/endangered/policies/index.html

USFWS. (2005). Revised Guidance on Site Assessments and Field Surveys for the

California Red-legged Frog. Retrieved October 21, 2006 from http://

www.fws.gov/sacramento/ es/documents/crf_survey_guidance_aug2005.pdf

USFWS. (2006). ESA Basics: 30 Years of Protecting Endangered Species. Retrieved

October 21, 2006 from http://www.fws.gov/Endangered/pubs/ESA BASICS_

050806.pdf

Burrowing owl (Athene cunicularia)

33

Appendix A: Acronyms________________________________

CDFG………………………………………………California Department of Fish and Game

CEQA……………………………………………………California Environmental Quality Act

CESA……………………………………………………..California Endangered Species Act

CNDDB…………………………………………………California Natural Diversity Database

CRF…………………………………………………………………..California red-legged frog

CWA…………………………………………………………………………….Clean Water Act

EIR……………………………………………………………….Environmental Impact Report

ESA……………………………………………………………….…..Endangered Species Act

HCP…………………………………………………………………Habitat Conservation Plan

IS……………………………………………………………………………………...Initial Study

MND………………………………………………………..….Mitigated Negative Declaration

ND…………………………………………………………………………Negative Declaration

NMFS………………………………………………………National Marine Fisheries Service

NOAA……………………….…………...National Oceanic and Atmospheric Administration

NRCS………………………………………………...Natural Resource Conservation District

NWP……………………………………………………………...…………..Nationwide Permit

RHA…………………………………………………………..Rivers And Harbors Act of 1899

RWQCB…………………………….…………………Regional Water Quality Control Board

SAA………………………………………………………….Streambed Alteration Agreement

SBCPW……………………………………………………...San Benito County Public Works

SCCRCD………………………………Santa Cruz County Resource Conservation District

TDS…………………………………………………….………………...Total Dissolved Solids

USACE……………………………………….……..United States Army Corps of Engineers

USFWS………………………………………………United States Fish and Wildlife Service

34

Appendix B: Wetland Creation__________________________

Wetlands can influence regional water flow regimes by intercepting and storing

storm waters, thereby changing sharp runoff peaks to slower discharges over longer

periods of time (Mitsch et al., 2000). Figure 1 shows some of the potential riparian

wetland values during both flood and dry seasons (Mitsch et al., 2000). During storm

events, wetlands have the

potential to reduce the damage

associated with flooding. For

example, Ogawa et al. (1986)

used a hydrologic simulation to

investigate the relationship

between upstream wetland

removal and downstream

flooding. They found a

significant increase in peak

streamflow for all streams when

wetlands were removed

upstream.

Mitsch et al. (2000) define two

basic principles for wetland restoration and creation:

• Those involved must have an understanding of the principles of wetland ecology, which include, but are not limited to, hydrology, biogeochemistry, adaptations, and succession.

Figure 1 Illustration of the potential wetland values for riparian wetlands during the a. flood season and b. dry season (After Mitsch et al., 2000)

35

• Those involved must resist the temptation to over-engineer by attempting either to channel natural energies that cannot be channeled or to introduce species that the landscape or climate do are unable to support.

In other words, human contribution to the design of wetlands should be kept simple

and not attempt to defy the natural ecological laws governing the landscape (Mitsch et

al., 2000).

The land surrounding Tequisquita Slough is believed to hold the potential to be an

established wetland. Installation of a tile drainage system that drains into the created

wetland could facilitate lowering the groundwater table depending on its construction

and water retention capacity (Figure 2). A levee or dike system could reduce the extent

of flooding on adjacent farmland (USDA, 2003). These activities would require

earthwork that is likely to be subject to CEQA and requires specialists trained in wetland

delineation and engineering.

Figure 2 Illustration of a lateral wetland intercepting groundwater carried by tile drains (After Mitsch et al., 2000)

36

Appendix C: Field Visits________________________________

From April through May of 2006, I made three site visits to Tequisquita Slough to

survey for CRF. The April visit was facilitated by Mary Ellen Dick, Central Coast

Agricultural Water Quality Coalition, Water Quality Coordinator, and served the purpose

of general reconnaissance to familiarize myself with the project site and its existing

conditions. We accessed the project site by navigating a kayak upstream to the

divergence of the natural and realigned channel. The natural channel was blocked by

dense strands of Typha spp., accumulated debris, and garbage, and the bottom was too

deep to reach by foot so we navigated the realigned channel. We then navigated

through dense thickets of Typha spp. towards the project site (Figure 1). The Typha

spp. grew too dense and the floor too deep,

and we were ultimately unable to reach the

original channel. The water was very

stagnant and bubbled with marsh gas.

My second and third visits occurred

during the beginning of May 2006. The

purpose was to establish a quick and safe

walking route from a landowner’s property

into the project site for nocturnal CRF eye

shine and auditory surveys. Prior to any

surveying, I was trained on CRF surveying

procedures by Antonia D’Amore, a CRF certified graduate student of the University of

California Santa Cruz, at her study site in Elkhorn Slough.

Figure 1 Mary Ellen Dick attempting to navigate through dense thickets of Typha spp. that effectively blocked the passage into the project site on April 5, 2006..

37

Entrance to the project site for

my second visit was through the

Chambers’ property that borders an

eastern portion of the slough. This

path turned out to be completely

blocked by Salix spp. whose

density forced the abandonment of

my route. I resolved to approach

the project site from the western

bank that borders Val Rocha’s property and follow the path from my first visit with Mary

Ellen Dick. Of all the landowners properties shallowly inundated by flood waters, it

appeared that Val Rocha’s property bared the largest burden. Figure 2 depicts an area

5 meters from the slough’s western bank that has been inundated by water. The red

stands of vegetation surrounding

the pool is the halophylic

Pickleweed (Salicornia virginica),

which is often found in areas of

high salinity and a continuous water

source (Mitsch et al., 2000).

Crossing eastward over the now

dry former channel, I navigated

upstream along the banks until

blocked by thickets of Typha spp.

Figure 2 Flood water from Tesqusiquita Slough that has begun encroaching onto Val Rocha's poperty. Conditions are saline indicated by the red strands of pickleweed (Salicornia virginica).

Figure 3 Dense thickets of Typha spp. lining the outside boundary of the project site.

38

and thick, stagnant mud. The Typha spp. was dense and you could see that little by little

the channel was being sedimented due to the vegetation’s effects on reducing water

velocity (Figure 3). As depicted in Figure 4, the ground surrounding the western edge of

the project site was shallowy inundated and mucky. However, it should also be noted

that field visits were made at the beginning of the dry season and water velocity likely

increases during the rainy season.

Since I could not find or make a

path into the project site, I resolved

that CRF auditory surveying was

my only alternative. However, on

my drive home I was overcome with

an intense allergic reaction to grass

pollen from Rocha’s field and

abandoned the surveying

altogether. Therefore, I can make no claim as to the existence of any CRFs within the

project site. I can only assert the importance of future surveillance.

Figure 4 Author of this paper standing in ankle deep mud just outside the western boundaries of the project site.

39

Appendix D: Permitting Flowchart_______________________