Vermillion River 2012 Fish Community Monitoring Report...The long-term biological monitoring...

Vermillion River 2012 Fish Community Monitoring Report

Wenck File #1305-16 DECEMBER 2012

Prepared for

Vermillion River Watershed Joint Powers Organiza on Physical Development Division—14955 Galaxie Avenue

Apple Valley, Minnesota 55124

Wenck File #1305-16

Prepared for:

VERMILLION RIVER WATERSHED JOINT POWERS ORGANIZATION

Vermillion River 2012 Fish Community

Monitoring Report

Prepared by:

WENCK ASSOCIATES, INC. 1800 Pioneer Creek Center

P.O. Box 249 Maple Plain, Minnesota 55359-0249

(763) 479-4200

December 2012

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Table of Contents

1.0 INTRODUCTION ........................................................................................................... 1-1

2.0 STREAM FISH MONITORING ................................................................................... 2-1

2.1 Field Reconnaissance and Reach Determination ................................................. 2-3 2.2 Fish Community Monitoring ............................................................................... 2-5

3.0 MONITORING RESULTS ............................................................................................ 3-1

3.1 Fish Community Summary Information .............................................................. 3-1 3.2 IBI Calculations ................................................................................................... 3-3

4.0 CONCLUSIONS .............................................................................................................. 4-1

5.0 REFERENCES ................................................................................................................ 5-1

TABLES

1 Sample reach information for the 14 stream fish monitoring sites 2 Electrofishing Methods and Sample Dates 14 stream fish monitoring sites 3 General Fish Community Sampling Results 14 stream fish monitoring sites 4 IBI scoring results for 14 stream fish monitoring sites applying the new MPCA statewide

IBI scoring protocol

CHARTS

1 Comparison of IBI Scores using the MPCA statewide protocol across 2009 to 2012 monitoring years

2 Comparison of IBI scores under MPCA statewide protocol to impairment listing thresholds for the fish community in the Southern Headwater Streams Category

3 Comparison of IBI scores under MPCA statewide protocol to impairment listing thresholds for the fish community in the Southern Streams Category

4 Comparison of IBI scores under MPCA statewide protocol to impairment listing thresholds for the fish community in the Southern Coldwater Streams Category

FIGURES

1 Stream Monitoring Sites in the Vermillion River Watershed 2 Stream Monitoring Site A1 3 Stream Monitoring Site A2

Table of Contents (cont.)

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4 Stream Monitoring Site A3 5 Stream Monitoring Site A4 6 Stream Monitoring Site A5 7 Stream Monitoring Site A6 8 Stream Monitoring Site A7 9 Stream Monitoring Site A8 10 Stream Monitoring Site A9 11 Stream Monitoring Site A10 12 Stream Monitoring Site A12 13 Stream Monitoring Site A13 14 Stream Monitoring Site A14 15 Stream Monitoring Site A15

APPENDICES

A Field Photos B MN DNR Special Survey Permit No. 18532 C Species Summary Table D Trout Collections Summary Table E MPCA State Wide Fish IBI Fact Sheet

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1.0 Introduction

The Vermillion River Watershed covers approximately 335 square miles in Scott and Dakota Counties in Minnesota and contains reaches designated as either warmwater or coldwater stream fish communities. The Vermillion River Watershed Joint Powers Organization (VRWJPO) is tasked with developing policies and programs that protect and improve water resources within the watershed. In the summer of 2008, the VRWJPO developed a biological monitoring plan as a means to assess and track biological health throughout the watershed. The biological monitoring plan describes goals and objectives for monitoring aquatic macroinvertebrate and fish community health as well as assessing the existing stream habitat and geomorphology in the watershed.

Because the Vermillion River Watershed contains stream reaches that are designated as both warmwater and coldwater fish communities, the VRWJPO is interested in determining the appropriate means for assessing the fish community health in both warmwater and coldwater reaches as well as establishing appropriate management goals for each community type. The Index of Biotic Integrity (IBI) is a useful tool that has been developed for assessing the overall health of a stream by monitoring some aspect of the biological community. IBIs have been developed for both warmwater and coldwater stream fish communities. The Minnesota Department of Natural Resources (MN DNR) is currently coordinating with the VRWJPO on the IBI monitoring. The VRWJPO has expanded their IBI monitoring program to monitoring sites in addition to what MN DNR personnel are currently providing.

In the summer and early fall of 2009, fish community monitoring was conducted by two parties for the VRWJPO; the MN DNR and Wenck Associates, Inc. (Wenck). Each party was responsible for conducting fish community monitoring at seven stream sampling locations in the watershed. Monitoring was again conducted by the MN DNR and Wenck in 2010, 2011 and 2012. In 2012 the VRWJPO began a watershed-wide study that will address a variety of water quality and biological impairments. The study will also development management goals for the Vermillion River watershed. This study is referred to as the Vermillion River Watershed Restoration and Protection Plan (WRAPP). The long-term biological monitoring program, including the fish and


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macro-invertebrate datasets will form the basis for the stressor identification process for the biological impairments. This report provides data analysis and summary of the 2012 fish community monitoring results as well as providing comparisons of the results to previous monitoring years.


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2.0 Stream Fish Monitoring

Fourteen stream monitoring sites were identified by the VRWJPO for inclusion in the 2009 fish

community monitoring project (Figure 1). In 2010, two changes were made to the 14 sites from

2009. The fish community monitoring in 2012 was conducted at the exact same 14 reaches as in

2010 and 2011 with the revisions from 2010 described as follows.

The first change was the relocation of site A10 approximately one-tenth of a mile downstream.

This reach was relocated due to site access issues. The new reach for A10 has not been

channelized (as the original A10 reach had) and contains a riparian zone of wetland and forest

vegetation as opposed to agricultural fields. Due to the close proximity of the relocated site to the

original site, data comparisons between the two reaches are appropriate.

The second change was the discontinuation of monitoring at site A11. This site is located on a

small tributary stream with limited habitat. Due to low water conditions at site A11, the fish

community was not monitored at this site in 2009. It was determined that this stream experiences

intermittent conditions during most years, and would not likely support a long term stable fish

community, and thus be an unlikely site for appropriate management or stream restoration

projects.

As a result, a new monitoring reach was established on Middle Creek in Farmington where

biomonitoring had not taken place as part of the biomonitoring plan implementation. This site

was labeled as site A15 (see Figure 1). The new A15 site provides a more visible site in the

watershed that is more likely to be the target of management dollars or projects by the VRWJPO,

MN DNR, or other partners.


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The fourteen monitoring sites include ten reaches (sites A1, A2, A3, A5, A6, A7, A8, A9, A12,

and A13) that are designated as coldwater fish communities (class 2A waters). The four

remaining reaches (sites A4, A10, A14 and A15) are classified as warmwater fish communities

(class 2B waters). Additionally there are 12 reaches that are designated as trout streams by the

MN DNR, sites A1, A2, A3, A5, A6, A7, A8, A9, A10, A12, A13 and A15. The MN DNR

designation of trout streams does not always follow the state beneficial use classification of 2A

coldwater communities, although classifying it as class 2A following a trout designation by the

DNR is the typical process for the MPCA. The MPCA Rulemaking process is proposing to

change any class 2B water that is currently a MN DNR designated trout stream to a class 2A

water, however this is still pending. If the MPCA were to implement the proposed rule changes,

some sites in the watershed could change from class 2B water to a class 2A water.

The fish community monitoring data that has been collected under the VRWJPO Biomonitoring

Plan was gathered for the intent of using the data to calculate Index of Biotic Integrity (IBI)

scores and making management decisions based on fish community health. IBI’s are tools that

are often used to assess the overall health of a water body based on the composition of a certain

facet of the biological community. During the 2009 and 2010 monitoring years there were two

fish community based IBI’s that were used to score each of the fourteen sampling reaches

monitored in the Vermillion River Watershed.

During past monitoring years two different IBI protocols, one warmwater protocol and one

coldwater protocol, were applied to the monitoring data at each site. The intent was to determine

type and health of the stream fish communities at the different reaches. The MPCA developed a

new state-wide IBI protocol in 2011. The intent of the updated IBI was to provide appropriate

scoring criteria to address all watersheds, rivers and streams across the State, including both

warmwater and coldwater systems. The data from 2009 through 2012 has been scored using the

new MPCA state-wide IBI scoring protocol. The database has not yet been released by the

MPCA allowing the general public to use the IBI protocol to score fish community datasets.

However, the MPCA has assisted the VRWJPO by completing the IBI scoring and providing the

individual metric scores to in order for the VRWJPO to further analyze and interpret the data.


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2.1 FIELD RECONNAISSANCE AND REACH DETERMINATION

The MPCA warmwater IBI (Nemila and Fiest, 2002) describes the methods for determining the

proper length of a stream sample reach necessary for fish community monitoring. Based on

previous studies in Wisconsin by Lyons (1992) the proper sample reach for IBI monitoring is 35

times the mean width of the stream. The MPCA has added an additional condition that the

minimum sample reach be no less than 150 meters and the maximum reach be no more than 500

meters (Niemela and Fiest, 2002). These reconnaissance and sampling methods were repeated in

2012.

For the seven stream reaches monitored by Wenck, field reconnaissance of the sample sites was

performed in August 2012. The seven sampling reaches were previously established during prior

years of the study. In 2009 and 2010, the width of the stream channel for each reach was

measured with a 300-foot survey tape a minimum of ten times for each sample reach. The

distance between channel width measurements varied from 50 to 100 feet, depending on the

average width of the stream. The channel width measurements were relatively consistent for the

sample sites, with all of the sites except site A14 averaging less than 15 feet in width. In 2012,

the widths of the reaches were “spot-checked” at several locations and found to be consistent

with the average width from previous monitoring years. The total reach sample length for each of

the seven sites monitored by Wenck was the same in 2012 as in previous years of the monitoring

program.

The seven stream reaches monitored by the MN DNR had been previously established during

brown trout assessment surveys, prior to the inception of the VRWJPO biological monitoring

program. The length of these sample reaches was determined based on the mark and recapture

surveys conducted for brown trout and not based on the MPCA protocol of 35 times the mean

width of the stream. These previously established sample reaches were surveyed by the MN

DNR as part of the IBI assessments.

Once the sample reaches were determined, flagging was placed on a tree along the bank at the

upstream and downstream end of the reach for each site. The GPS coordinates were recorded


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with a hand-held GPS unit at the upstream and downstream points (Table 1). Photos of the

sample reaches from 2012 are provided in Appendix A (field photos 1 - 7).

Table 1: Sample reach information for the fourteen sites in the 2012 Vermillion River stream fish monitoring project.

Site

Stream

Classification Upstream Coordinates Downstream Coordinates

Average

Width

Sample Reach

Length (meters)

A1 Coldwater 44.619 -93.218 44.619 -93.216 12.9 ft 492 ft (150 m)

A2 Coldwater 44.640 -93.219 44.639 -93.216 9 ft 1120 ft (341 m)


A4 Warmwater 44.609 -93.192 44.610 -93.192 7.4 ft 492 ft (150 m)


A6 Coldwater 44.639 -93.157 44.639 -93.154 22 1350 ft (411 m)







A14 Warmwater 44.686 -92.956 44.687 -92.955 35 ft 1225 ft (373 m)


A special permit from the MN DNR is required for private entities or individuals to conduct fish

community monitoring such as electrofishing in Minnesota public waters. A letter and map of

the sample sites was sent to the MN DNR on July 10th, 2012 by Wenck requesting a permit to

conduct fish community monitoring at the seven designated sites on the Vermillion River by

means of backpack or barge electrofishing. The special survey permit was issued by the MN

DNR on July 13th, 2012 (see Appendix B). The survey permit is valid until the end of the

calendar year and must be renewed for future years of the study. The survey permit also requires

that the fish community data collected be reported to the MN DNR. Survey results from this

report were provided to the MN DNR to fulfill that requirement.


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2.2 FISH COMMUNITY MONITORING

The index period for fish community sampling is defined as mid-June through mid-September in

the previous MPCA warmwater IBI protocol. The sampling index period for the new State-wide

IBI developed by the MPCA is not yet available. The MN DNR has conducted monitoring in the

Vermillion River, traditionally sampling in late August through early September. In 2012, the

IBI fish community monitoring efforts were conducted from late August through mid-September

to correspond to the previous years of DNR monitoring, as well as previous years of monitoring

under the VRWJPO monitoring program.

The application of the different sampling methods are defined in the MPCA warmwater IBI

based on stream size (Niemela and Fiest, 2002), with the backpack unit used for small, wadeable

streams less than eight meters wide and the barge unit used on medium sized, wadeable streams

greater than eight meters wide. The fish sampling methods for the new MPCA IBI scoring

protocol were kept the same as the previous versions of the IBI. The backpack unit was used at

ten sites, (see Appendix A – photo 8), while the barge unit was used at four sites (see Appendix

A – photo 9).

All stream fish collections followed the methods outlined in the MPCA warmwater IBI, as well

as the MPCA Standard Operating Procedures for electrofishing (Rev. Feb. 2009). Each reach

was fished beginning from the downstream point established during field reconnaissance in an

upstream direction up to the upstream end of the established reach. All habitats within the

channel were sampled with the electrofishing units and all fish were netted during fishing. Due to

the relatively narrow width of most of the stream reaches, it was possible to effectively sample

all available instream habitats. The electrofishing method and sample dates for each reach are

presented in Table 2.


2-6

Table 2: Electrofishing methods and sample date for the 14 sites in the 2012 Vermillion River stream fish monitoring project. Site Stream Classification Sampling Method Sample Date

A1 Coldwater Backpack Unit 08/29/2012



A4 Warmwater Backpack Unit 08/29/2012


A6 Coldwater Barge Unit 09/07/2012







A14 Warmwater Barge Unit 09/21/2012


All fish were placed in buckets or tubs and water in the buckets was changed during monitoring

to provide adequate dissolved oxygen for the fish. For reaches where electrofishing lasted more

than one half hour or when a large number of fish were collected, large tubs were set up with

aerators. Fish mortality was negligible, with only a few individual deaths during all of the

collecting.

After electrofishing was complete, a fish processing station was set up (see Appendix A – Photo

10) whereby all individuals were identified and sorted by species into a separate tub/bucket. Dr.

Patrick Ceas of St. Olaf College served as the expert ichthyologist for reaches monitored by

Wenck. Once the identification and sorting was complete, the largest and smallest individuals of

each species were weighed and measured, following the MPCA protocols (see Appendix A –

Photo 11). Batch weights were then taken of the remaining individuals for each species.

In some cases large fish were weighed and measured individually. In most cases all trout

collected were weighed and measured individually. All fish of each species were then counted


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and released. All fish community data collected, including fish species, number of each species,

lengths and weights were recorded on MPCA datasheets for stream fish monitoring.


3-1

3.0 Monitoring Results

3.1 FISH COMMUNITY SUMMARY INFORMATION

There were a total of 2,632 fish collected from 22 different species across the 14 sites that were

monitored in 2012 (see Appendix C – Species Summary Table). Species diversity ranged from a

low of four species collected at site A1 to a high of 15 species collected from sites A5 (Table 3).

Total fish collected ranged from a low of eight fish collected from site A1 to a high of 483 fish

collected from site A5 (Table 3).

Table 3: General fish community sampling results for the 14 sites in the 2012 Vermillion River stream fish monitoring project.

Site Stream Classification MN DNR

Trout Stream Total

Species Total Fish A1 Coldwater Yes 4 8

A2 Coldwater Yes 8 115


A4 Warmwater No 10 422






A10 Warmwater Yes 11 120



A14 Warmwater No 13 304

A15 Warmwater Yes 8 89

All Sites -- -- 22 2,632


3-2

The most abundant fish of the 2012 sampling were green sunfish, totaling 826 fish or 31 percent

of the total catch. White suckers were the second most abundant fish collected in 2012, totaling

657 individuals and comprising 25 percent of the total catch. Fathead Minnows were the third

most abundant fish collected in 2012, totaling 223 or about nine percent of the combined total

catch for all 14 sites. Brown trout accounted for about eight percent, central mudminnows

accounted for 6.4 percent, and johnny darters accounted for approximately five percent of the

total combined catch. All other individual species comprised less than five percent of the

combined total catch for the 14 monitoring sites (see Appendix C).

During the 2012 sampling, green sunfish, central mudminnows and white suckers were the three

species collected at all of the 14 monitoring sites. These species have been among the most

widespread in terms of sites across most monitoring years of the project; however 2012 is the

first year where all three species were collected at every site. Iowa darters were collected from

11 of the 14 monitoring sites in 2012 (see Appendix C – Species Summary Table). Iowa darters

are one of the few species rated as sensitive that are collected in the watershed. Brown trout,

fathead minnows and largemouth bass were collected at 10 sites. Northern Pike and johnny

darters were collected from eight sites, while bluegills were collected from seven sites. The other

12 of the 22 species observed during the 2012 Vermillion River fish monitoring were collected at

six or fewer sites (see Appendix C – Species Summary Table).

Brown trout were collected from 10 sites during the 2012 study, of which eight are classified as

coldwater fish communities (sites A2, A3, A5, A6, A6, A8, A12 and A13), and from two sites

that is classified as having a warmwater fish community (site A10 and A14). Based on previous

MN DNR sampling efforts, it is not uncommon to collect an occasional brown trout on the main

stem of the Vermillion River in the lower reaches of the watershed that are classified as

warmwater fisheries. Additionally, A10 is currently classified as a warmwater reach but is a

tributary to the South Branch of the Vermillion River and trout have been consistently collected

from this reach.


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The largest brown trout collected in 2012 was a 24 inch trout collected at site A3. The large

female trout found at site A3 the three previous years of the study was not observed in 2012. Site

A3 has consistently produced some of the largest trout captured during all years of the study.

Other large trout collected during the study include 19, 18, 17 and 16-inch trout collected at site

A2, one 18-inch and one 16-inch trout at site A3, 18-inch and 16-inch trout collected from site

A10, and a 21-inch trout collected at site A12. See Appendix D for a summary of all trout

collected during the study.

3.2 IBI CALCULATIONS

The 2012 Vermillion River stream fish monitoring project included stream monitoring sites

designated as either warmwater or coldwater fish communities. The purpose of the monitoring

was to collect stream fish community datasets to be used to calculate IBI scores for each sample

site. During previous years of the study, both coldwater and warmwater IBI scoring criteria were

applied to the fish community monitoring data at each reach to assist the VRWJPO in

determining appropriate management goals for the stream fish communities throughout the

watershed.

In 2011 the MPCA released a draft pamphlet outlining some of the information for a new set of

IBI scoring criteria to cover all rivers and streams, both warmwater and coldwater, across the

State of Minnesota. Under the new MPCA statewide IBI, each monitoring reach will be scored

with only one set of metrics appropriate to the size of the stream and the type of fish community

(warmwater versus coldwater). The application of the appropriate MPCA stream category

scoring protocol matches the criteria the MPCA is using to list the impairment designations for

the Vermillion River watershed. The results from the 2012 monitoring are discussed in the

context of the new MPCA Statewide IBI scoring protocols and along with all years of the

monitoring data from the Vermillion River biological monitoring program.


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The MPCA has developed nine stream categories across two geographic regions: Northern and

Southern. There are four stream categories in each region and one statewide category, termed

“low gradient” streams. All of the 14 stream monitoring sites in the Vermillion River fall into the

Southern geographic region. The 14 sites are within the following three categories: Southern

Headwaters; Southern Streams; or Southern Coldwater. Streams within the Southern Headwaters

category are defined as small to moderate, high gradient, warm/cool water streams in southern

Minnesota with a watershed area less than 30 square miles. Three Vermillion River monitoring

reaches, A4, A10, and A15, are within this category.

Streams within the Southern Streams category are defined as large warm/cool water streams and

small rivers in southern Minnesota where the watershed area is greater than 30 but less than 300

square miles. Only Site A14, which is a sample reach on the main stem of the Vermillion River

in the lower quarter of the overall watershed, falls within this category. The streams within the

Southern Coldwater category include all coldwater streams in southern Minnesota. This category

does not include a watershed size requirement. There are ten monitoring reaches in the

Vermillion River that fall within this category, including sites A1, A2, A3, A5, A6, A7, A8, A9,

A12 and A13.

During previous years, the IBI scoring criteria were applied to the fish monitoring data within a

spreadsheet and the warmwater and coldwater scores were calculated for each reach. The scoring

criteria, metrics and methodology for the new MPCA Statewide IBI are not yet available to the

public. As a result, in 2011 the IBI scores for the 14 sample sites were calculated by the MPCA

and submitted to the VRWJPO. The MPCA scored the monitoring data for all three of the

previous monitoring years, applying the appropriate stream scoring criteria (i.e. Southern

Headwaters; Southern Streams; or Southern Coldwater) to each site. In 2012, VRWJPO

submitted the data to the MPCA and again scored the data from 2012 for all sites. The IBI scores

using the new MPCA statewide criteria are provided in Table 4, comparing all four years of

monitoring data.


3-5

Table 4: IBI scores calculated using the new MPCA Statewide IBI scoring criteria for all fish community monitoring sites from the Vermillion River stream fish monitoring project from 2009 through 2012.

Site Stream

Classification MPCA IBI Category 2009 IBI 2010 IBI 2011 IBI 2012 IBI

Listing Threshold

A1 Coldwater Southern Coldwater 41 33 45 39 <45



A4 Warmwater Southern Headwaters 73 75 75 61 <51






A10 Warmwater Southern Headwaters 80 74 80 80 <51



A14 Warmwater Southern Streams 43 38 40 47 <45

A15 Warmwater Southern Headwaters -- 75 75 71 <51

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4-1

4.0 Conclusions

Fish community monitoring was conducted at 14 stream sites during the 2012 Vermillion River

stream fish monitoring project. A statewide IBI scoring criteria developed by the MPCA was

applied to monitoring data from 2012 as well as previous monitoring years. A comparison of the

IBI scores for each of the 14 monitoring sites across all three monitoring years is provided as

Chart 1. The monitoring sites from the Vermillion River watershed fall into three different

stream categories from the MPCA IBI protocol: Southern Headwater Streams; Southern Streams

and Southern Coldwater Streams. Each of the three stream categories uses a different set of

scoring metrics, appropriate for that stream category. In 2012, the MPCA provided the VRWJPO

with the scoring results from the individual metrics for each of the 14 monitoring reaches for all

four years of the monitoring program. Analysis of the metric scoring for the sites from each

category is provided.

Chart 1: Comparison of IBI scores under the new MPCA Statewide scoring criteria across four monitoring years (2009-2012).

0

10

20

30

40

50

60

70

80

90

A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A12 A13 A14 A15

IBI Scores

Monitoring Station

2009

2010

2011

2012

Impairment Threshold


4-2

Southern Headwater Streams

There are three monitoring reaches within the Southern Headwaters category, sites A4, A10 and

A15. All three of these stream sites scored high under the new MPCA Statewide IBI scoring

criteria, with scores ranging from 61 to 80 in 2012. The threshold for listing of the fish

community as impaired is 51 or below (see Table 4 and Chart 2) within this stream category. All

three streams scored well above the listing threshold during all four monitoring years. There are

seven metrics for streams in the Southern Headwaters category listed in the MPCA IBI scoring

(Sandberg, 2011):

• Relative abundance (%) of taxa that are Detritivores

• Relative abundance (%) of individuals with DELT Anomalies

• Relative abundance (%) of taxa that are Generalist Feeders

• Taxa richness of Sensitive species

• Relative abundance (%) of individuals that are short-lived

• Relative abundance (%) of individuals that can spawn multiple times

• Relative abundance (%) of taxa that are Very Tolerant

The total score for the IBI is 100. One of the metrics, abundance of DELT Anomalies has a score

of zero unless anomalies are present, in which case negative points are given. The remaining six

metrics add up to the max score of 100, which makes each metric worth a maximum of 16.7.

The three stream reaches in the Southern Headwater Streams Category have been scoring very

well across all four years of monitoring data and therefore are receiving high individual scores

for many of the metrics. Specific metrics that are scoring particularly well include: relative

abundance of taxa that are generalist feeders; relative abundance of individuals that are short

lived; and relative abundance of individuals that are serial spawners (multiple times per year).

All three of these metrics have a “negative” relationship, indicating that as the percentage of

these individuals increase in the overall total catch the metric score goes down. Alternately, as

these individuals comprise a lower number of the total catch the metric score increases. Some of

the species that are classified within these metrics are present in the Vermillion River watershed,

however, they are comprising a small enough percentage of the total catch at the Southern


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Headwater reaches that the metric scores are high, resulting in high total IBI scores for these

sites.

Chart 2: Comparison of the Southern Headwater Streams IBI scores under new MPCA statewide protocol to impairment listing thresholds.

Southern Streams

Site A14 is the only warmwater stream reach within the South Streams category. This site is on

the main stem of the Vermillion River and is currently located the farthest downstream in the

overall watershed. The threshold for listing of the fish community within this stream category as

impaired is 45 or below (see Table 4 and Chart 3). Site A14 scored below the impairment listing

threshold during the first three monitoring years, but was above the impairment threshold in

2012 for the first time with a score of 47. There are nine metrics in the Southern Streams

category of the MPCA IBI (Sandberg, 2011):

• Relative abundance (%) of taxa Benthic Insectivores (excludes tolerant)


73 80

0

75 74

75 75 80

75

61

81

71

0

10

20

30

40

50

60

70

80

90

A4 A10 A15

IBI S

ocre

Monitoring Station

2009

2010

2011

2012

Impairment Threshold: 51

Score below 51 considered impaired

Score above 51 considered healthy


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• Relative abundance (%) of individuals with a female mature age <=2


• Relative abundance (%) of taxa that are Sensitive

• Taxa richness of short-lived species

• Relative abundance (%) of taxa that are Tolerant

• Relative abundance (%) of individuals that are Tolerant

• Relative abundance (%) of individuals the dominant 2 species

The Southern Streams category again uses the DELT anomalies metric, which gives a zero or

negative score. The other eight metrics add up to a total of 100, which equates to a max metric

score of 12.5. Site A14 has generally scored low on many of the above metrics. The overall IBI

scores at site A14 appear to be driven by moderately high scores for the relative abundance of

taxa that are detritivores and also by the low to very low scores for the relative abundance of taxa

that are sensitive, relative abundance of taxa that are tolerant, relative abundance of individuals

that are tolerant and relative abundance of the dominant two species.

Chart 3: Comparison of the Southern Streams IBI scores under new MPCA statewide protocol to impairment listing thresholds.

43 38 36

47

0

10

20

30

40

50

60

70

80

90

100

A14

IBI S

core

Monitoring Station

2009

2010

2011

2012Impairment Threshold: 45



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4-5

In general the relative high percentage of tolerant species (i.e. taxa) and tolerant individuals, as

well as the low number of sensitive species is keeping the overall IBI score at site A14 low and

in general below the impairment threshold.

Southern Coldwater Streams

The ten remaining stream reaches fall within the Southern Coldwater Streams category. Among

the ten monitoring sites in the Southern Coldwater Streams category, there is low to moderate

variation in the IBI scores across years (see Chart 4). The threshold for listing of the fish

community as impaired is 45 or below (see Table 4 and Chart 4) within this stream class. Due to

the moderate variation in the IBI scores for the streams in this class, many of the streams had

scores both above and below the threshold over the four years of monitoring including sites A3,

A8, A9, A12 and A13. Other sites such as A2 and A6 scored below the listing threshold all four

years of the study.

Chart 4: Comparison of IBI scores under MPCA statewide protocol to impairment listing thresholds for the fish community in the Southern Coldwater Streams Category

4136

42

45

34

40

51

42 40

46

33

42

55

40

36

45

39

49

38

4845

43

52

36

41

36

48

38 41 423938

42

34 33 34

39

29

49

29

0

10

20

30

40

50

60

70

80

90

100

A1 A2 A3 A5 A6 A7 A8 A9 A12 A13

IBI Score

Monitoring Station

2009

2010

2011

2012

Impairment Threshold: 45




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There are eight metrics used in the Southern Coldwater Streams IBI category (Sandberg, 2011):

• Relative abundance (%) of individuals that are Sensitive in coldwater streams

• Number of taxa that are Tolerant in coldwater streams


• Relative abundance (%) individuals that are Herbivores

• Relative abundance (%) of individuals that are Native Coldwater species

• Relative abundance (%) of taxa that are Native Coldwater species

• Relative abundance (%) of individuals that are Pioneer species


The Southern Coldwater Streams category again uses the DELT anomalies metric, which gives a

zero or negative score. Therefore the other seven metrics add up to a total of 100, which equates

to a max metric score of 14.3. All ten of the coldwater reaches are generally scoring at or below

the impairment threshold, indicating that the streams are scoring poorly on several metrics while

scoring well on only a few metrics. The main metrics that appear to be driving the coldwater IBI

scores in the Vermillion River include moderately good scores for the relative abundance of

herbivore species and relative abundance of pioneer species, along with low to very low metric

scores for the relative abundance of native coldwater taxa (i.e. species) and relative abundance of

native coldwater individuals. Metric scores for abundance of sensitive individuals and number of

coldwater tolerant taxa varied from year to year across sites but in general resulted in low overall

scores.

The high scores for the abundance of herbivore species and relative abundance of pioneer species

are for metrics that have a negative relationship. The coldwater sites are scoring well for both of

these metrics due to the low number or complete absence of these species and individuals. It is

likely that the sites will continue to always score well on these metrics in the future as the species

that comprise these metrics are not prevalent or even absent from the watershed.


4-7

The most abundant coldwater species in the Vermillion River watershed is the brown trout,

which is an introduced species. As a result it is not counted in the native coldwater taxa or

individuals metrics. There are two native coldwater species that have been collected during the

biological monitoring program, the brook stickleback and the pearl dace. These two species are

currently very limited within the watershed in terms of distribution and total individuals. For

example in 2012, brook stickleback were collected from only five sites with only ten individuals

collected and pearl dace were collected at only two sites with five total individuals. By contrast,

the brown trout were collected at ten of the 14 sites and there were 209 individuals collected. The

two native coldwater species metrics account for almost 30 percent of the total IBI score and

most reaches are scoring zero out of 14 almost every year for the native coldwater individuals

metric and zero to five most years for the native coldwater taxa metric.

There are nineteen total species in the native coldwater species metric. A review of the MN DNR

FishMapper (http://www.dnr.state.mn.us/map/form/mapper.html) was conducted to query for

potential collection records of all of the 19 species includes in the MPCA native coldwater

species metric. The two species main that have been document in the Vermillion River during

recent or historical collections include the brook stickleback and the pearl dace. There is one

record of a brook trout collected by the MN DNR in 2004, which was likely associated with a

stocking effort that was conducted by the DNR in an attempt to establish brook trout in the

Vermillion River. There are no collection records of the other 19 species on the used in the

native coldwater species metrics. Based on known species range distributions, it is unlikely that

the 16 native coldwater fish with no recorded collections were ever present in the Vermillion

River Watershed. Species such as redside dace are found in watersheds to the south, such as the

Cannon River but have never been collected in the Vermillion River and likely never occurred

there. Other species such as finescale dace are found in the northern part of Minnesota and

species such as fantail darters and mottled sculpin are not found in low gradient streams such as

the Vermillion River. The very low number of native coldwater species that have either

historically occurred or currently exist in the watershed is limiting the IBI scores of the

coldwater streams. This indicates it would be difficult to increase the IBI scores to above the

impairment threshold.

http://www.dnr.state.mn.us/map/form/mapper.html


4-8

The coldwater stream reaches are also receiving relatively low scores for the taxa richness of

tolerant species in coldwater streams and relative abundance of individuals that are sensitive in

coldwater streams. Over the course of the biological monitoring program a fairly large number of

tolerant species and individuals have been collected from all sites in the watershed, including

tolerant warmwater species found in coldwater reaches. Additionally, there have been very few

species rated as sensitive found in the watershed. The only coldwater species rated as sensitive

collected in the Vermillion River watershed over the course of the monitoring program is the

pearl dace, which has been collected at a very low rate in terms of distribution across sites and

total individuals collected.

Conclusions

When applying the MPCA Statewide IBI scoring protocol the 14 monitoring sites within the

Vermillion River Watershed exhibit small to moderate amounts of variation in their scoring in

each stream category. In general, the warmwater steams in the South Headwater Streams

category had consistently high scores, above the impairment listing threshold for all sites for all

years of the monitoring program. The mainstem of the Vermillion River downstream of Highway

52 is the only portion of the watershed in the Southern Streams category. Most years this portion

of the river has fallen below the impairment threshold due to the prevalence of tolerant species

and the limited presence of sensitive species.

The monitoring reaches within the Southern Coldwater Streams category also scored consistently

using the MPCA IBI protocol, in general scoring at or below the impairment listing threshold

with little variation across monitoring years. The coldwater reaches are currently being limited

by the very low number and distribution of native coldwater species and individuals, as well as

sensitive coldwater species and individuals, in the Vermillion Watershed. The MPCA is

currently undergoing a revision to their rulemaking process that has the potential to change the

status of some 2B waters over to 2A waters, which would change the IBI scoring metrics applied

to the reaches. If the status of current steams within the Southern Headwater Streams category

were switched over to a 2A water and scored under the Southern Coldwater Streams category, it

is likely that the IBI scores would decrease and may fall below the impairment threshold.


5-1

5.0 References

Fish Community Sampling Protocol For Stream Monitoring Sites. (Revised February 2009). Minnesota Pollution Control Agency: Biological Monitoring Program.

Sandberg, J. 2011. Fish Indices of Biotic Integrity (F-IBI) used to assess streams and rivers in the

State of Minnesota. Minnesota Pollution Control Agency. Lyons, J. 1992. The Length of Stream to sample with towed electrofishing unit when fish species

richness is estimated. North American Journal of Fisheries Management. Vol. 12. pp. 198-203.

Mundahl, Neal D. and Simon, Thomas P. 1999. Development and Application of an Index of

Biotic Integrity for Coldwater Streams of the Upper Midwestern United States. pp. 383-415 In Thomas P. Simon (ed.) “Assessing the Sustainability and Biological Integrity of Water Resources Using Fish Communities”. CRC Press. Boca Raton, FL.

Niemela, Scott and Fiest, Michael D. 2002. Index of Biological Integrity Guidance for Coolwater

Rivers and Streams of the Upper Mississippi River Basin. Minnesota Pollution Control Agency: Biological Monitoring Program.

Figures

VERMILLION RIVER WATERSHED JPO2012 Fish Monitoring Sites

DEC 2012Figure 1Engineers - Scientists

Business Professionalswww.wenck.com

1800 Pioneer Creek CenterMaple Plain, MN 55359-04291-800-472-2232

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VERMILLION RIVER WATERSHED JPO2012 Fish Monitoring Site A1

DEC 2012Figure 2

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Appendix A

Field Photos

Photo 1: Site A1 Photo 2: Site A3



Photo 7: Site A15 Photo 8: Back-pack unit at Site A15

Photo 9: Barge-unit set up at Site A14 Photo 10: Fish processing at Site A10

Photo 11: Weighing Trout at Site A3

Appendix B

MN DNR Special Survey Permit

No. 18532

Appendix C

Species Summary Table

T:\1305 Dakota\16\Report\App C_Species Summary Table

Species Summary Table for Fourteen monitoring SitesVermillion River 2012 Fish Monitoring Study

Species Combined

Total CatchPercentage of

Total CatchNumber of

Sites Observed SitesBigmouth Shiner 22 0.8% 3 A5, A8, A14Black Bullhead 27 1.0% 6 A2, A4, A5, A6, A9, A13Blacknose Dace 2 0.1% 1 A7Bluegill 21 0.8% 7 A4, A5, A6, A7, A8, A14, A15Bluntnose Minnow 52 2.0% 3 A8, A9, A14Brook Stickleback 10 0.4% 5 A3, A5, A10, A13, A15Brown Trout 209 7.9% 10 A2, A3, A5, A6, A7, A8, A10, A12, A13, A14Central Mudminnow 169 6.4% 14 All SitesCommon Carp 22 0.8% 2 A7, A9Creek Chub 12 0.5% 5 A2, A4, A5, A8, A10Fathead Minnow 223 8.5% 10 A3, A4, A5, A6, A7, A8, A9, A10, A13, A14Golden Shiner 11 0.4% 5 A2, A5, A8, A9, A15Green Sunfish 826 31.4% 14 All SitesHybrid Sunfish 6 0.2% 1 A4Iowa Darter 113 4.3% 11 A1, A3, A4, A5, A6, A7, A8, A9, A10, A14, A15Johnny Darter 137 5.2% 8 A5, A6, A8, A9, A10, A12, A13, A14Largemouth Bass 69 2.6% 10 A3, A4, A5, A6, A7, A8, A9, A12, A14, A15Northern Pike 33 1.3% 8 A2, A5, A6, A7, A8, A9, A12, A13Northern Red Bellied Dace 3 0.1% 1 A10Pearl Dace 5 0.2% 2 A10, A14Tadpole Madtom 3 0.1% 1 A14White Sucker 657 25.0% 14 All Sites

2632 100.0%

Appendix D

Trout Collections Summary Table

Brown Trout Summary Table for all Six monitoring SitesVermillion River 2012 Fish Monitoring Study

Site Fish Length (in) Length (mm)Site A1 No Brown Trout Collected -- --Site A2 Brown Trout 19.0 482

Brown Trout 15.0 381Brown Trout 4.2 106Brown Trout 3.9 100Brown Trout 4.5 115Brown Trout 4.3 109Brown Trout 14.1 357Brown Trout 14.9 378Brown Trout 4.6 117Brown Trout 4.4 112Brown Trout 4.5 114Brown Trout 17.3 439Brown Trout 13.7 348Brown Trout 16.2 412Brown Trout 4.5 114Brown Trout 9.8 249Brown Trout 6.0 152Brown Trout 5.9 149Brown Trout 5.6 142Brown Trout 15.5 393Brown Trout 5.0 127Brown Trout 12.9 328Brown Trout 18.5 470Brown Trout 14.7 373Brown Trout 13.3 337Brown Trout 15.4 391Brown Trout 14.9 378Brown Trout 16.0 405Brown Trout 11.4 289Brown Trout 10.3 261Brown Trout 4.5 113Brown Trout 4.8 122Brown Trout 5.0 128Brown Trout 5.1 130Brown Trout 4.6 116Brown Trout 4.7 120Brown Trout 5.6 142

Site A3 Brown Trout 16.7 425Brown Trout 15.4 392Brown Trout 14.8 375Brown Trout 12.6 321Brown Trout 11.2 285Brown Trout 12.8 324Brown Trout 24.2 615Brown Trout 18.4 467Brown Trout 10.8 275Brown Trout 7.2 184Brown Trout - Avg for 28 Young of Year Fish 5.5 140


Site Fish Length (in) Length (mm)Site A4 No Brown Trout Collected -- --Site A5 Brown Trout 5.0 128

Brown Trout 4.9 124Brown Trout 5.3 134Brown Trout 4.1 104Brown Trout 5.4 136

Site A6 Brown Trout 5.0 126Brown Trout 4.8 122Brown Trout 5.3 135

Site A7 Brown Trout 10.8 273Brown Trout 5.0 126

Site A8 Brown Trout 11.0 278Brown Trout 6.6 167Brown Trout 5.2 133Brown Trout 5.2 131

Site A9 No Brown Trout Collected -- --Site A10 Brown Trout 17.9 455

Brown Trout 16.0 405Brown Trout 10.8 274Brown Trout 11.2 283Brown Trout 10.6 270Brown Trout 8.0 204

Site A12 Brown Trout 21.2 539Brown Trout 11.2 284Brown Trout 4.2 106Brown Trout 11.0 280Brown Trout 13.0 330Brown Trout 13.9 353Brown Trout 9.1 231Brown Trout 11.8 300Brown Trout 6.0 153Brown Trout 4.1 105Brown Trout 4.4 112Brown Trout 4.1 104Brown Trout 4.1 105Brown Trout 12.9 327Brown Trout 9.1 230Brown Trout 4.1 105Brown Trout 7.3 185Brown Trout 4.6 116


Site Fish Length (in) Length (mm)Site A13 Brown Trout 11.3 287

Brown Trout 8.4 213Brown Trout 7.1 179Brown Trout 8.8 223Brown Trout 4.7 120Brown Trout 4.1 105Brown Trout 5.1 130Brown Trout 4.4 112Brown Trout 3.6 92Brown Trout 4.5 115Brown Trout 4.3 108Brown Trout 4.6 116Brown Trout 4.6 116Brown Trout 12.5 316Brown Trout 12.6 319Brown Trout 14.8 375Brown Trout 9.5 242Brown Trout 9.7 246Brown Trout 8.8 224Brown Trout 9.6 243Brown Trout 7.7 196Brown Trout 4.1 105Brown Trout 4.5 115Brown Trout 4.2 107Brown Trout 4.0 101Brown Trout 4.7 119Brown Trout 4.1 105Brown Trout 5.6 141Brown Trout 5.4 138Brown Trout 8.4 212

Site A15 No Brown Trout Collected -- --Site A14 Brown Trout 4.9 124

brown Trout 5.0 128Brown Trout 5.2 132Brown Trout 5.4 138Brown Trout 5.7 144

Appendix E

MPCA State Wide Fish IBI Fact Sheet

The following document provides an overview of recently‐developed Fish Indices of Biotic Integrity (F‐

IBI) used to assess streams and rivers in the State of Minnesota. Complete documentation of the F‐IBI,

including information regarding development, calibration, scoring and application will be available in

2012. Any questions regarding this document or the F‐IBI in general may be referred to:

John Sandberg

Minnesota Pollution Control Agency

Brainerd, MN

218‐316‐3913

[email protected]

1

For the purposes of F‐IBI development, Minnesota’s streams and rivers were partitioned into nine

classes, across two geographic regions.

Southern Classes

Southern Rivers

Southern Streams

Southern Headwaters

Southern Coldwater

Northern Classes

Northern Rivers

Northern Streams

Northern Headwaters

Northern Coldwater

Statewide

Low Gradient

The classification framework partitions natural variability in fish community structure, based largely on

patterns observed among least‐impacted sites. Fish communities occurring at sites within each class are

more similar to each other than to those in other classes. The classification factors are unaffected by

human disturbance to ensure that the framework reflects natural variability and that the resulting F‐IBI

reflect impacts.

Regionalization largely follows major watershed boundaries and reflects significant post‐glacial barriers

to fish migration (e.g. St. Anthony Falls). Classification criteria are briefly described within individual

one‐page summaries and a complete “classification key” is available on page 9 including a map of the

geographic regions and the relevant watershed area and reach gradient thresholds.

F‐IBI development was stratified by class, with a unique suite of metrics, scoring functions, impairment

thresholds, and confidence intervals identified for each. Metric lists and descriptions are included in the

individual class summaries, as well as impairment thresholds and 90% confidence limits for F‐IBI score.

Lists of species associated with each metric are available upon request. F‐IBI scores higher than the

upper confidence limit reflect good biological condition, while scores below the lower confidence limit

reflect poor biological condition. When F‐IBI scores fall within the confidence interval, interpretation

and assessment of waterbody condition involves consideration of potential stressors, and draws upon

additional information regarding water chemistry, physical habitat, land use activities, etc. Assessment

decisions are made by MPCA’s Watershed Assessment Teams; documentation for the Water Quality

Assessment process can be found at:

http://www.pca.state.mn.us/index.php/water/water‐types‐and‐programs/minnesotas‐impaired‐waters‐

and‐tmdls/assessment‐and‐listing/tmdl‐water‐quality‐assessment.html

2

Southern Rivers

Classification Criteria:

Large warm/coolwater rivers in southern MN and the western portion of the Red River Basin

Sites in southern Minnesota and the Glacial Lake Agassiz Basin (GLAB) ecoregion, where

watershed area exceeds 300 square miles.

Examples:

Red River of the North, Minnesota River, St. Croix River (below Taylors Falls), Red Lake River

(within GLAB), Blue Earth River, Chippewa River, Otter Tail River (within GLAB), Zumbro River

Exclusions:

Mississippi River (below St. Anthony Falls), Minnesota River (above Laq qui Parle confluence)

Biocriteria:

Upper CL: 50

Impairment threshold: 39

Lower CL: 28

MetricName Category Response Metric_Desc_tech

DetNWQTXPct trophic negative Relative abundance (%) of taxa that are detritivorous

GeneralPct trophic negative Relative abundance (%) of individuals that are generalist feeders

Insect‐TolPct trophic positive Relative abundance (%) of individuals that are insectivore species (excludes tolerant species)

Piscivore trophic positive Taxa richness of piscivorous species

SLvdPct life history negative Relative abundance (%) of individuals that are short‐lived

SSpnTXPct reproductive negative Relative abundance (%) of taxa that are serial spawners (multiple times per year)

TolPct tolerance negative Relative abundance (%) of individuals that are tolerant

VtolTXPct tolerance negative Relative abundance (%) of taxa that are very tolerant

SensitiveTXPct tolerance positive Relative abundance (%) of taxa that are sensitive (scoring adjusted for gradient)

SLithop reproductive positive Taxa richness of simple lithophilic spawning species (scoring adjusted for gradient)

DomTwoPct dominance negative Combined relative abundance of two most abundant taxa

FishDELTPct tolerance negative Relative abundance (%) of individuals with Deformities, Eroded fins, Lesions, or Tumors

3

Southern Streams


Large warm/coolwater streams and small rivers in southern MN and the far‐western portion of

the Red River Basin


watershed area exceeds 30 square miles but is less than 300 square miles.

Examples:

Cobb River, Tamarac River, Sleepy Eye Creek, Middle River, Rock River, Hawk Creek, Minnehaha

Creek, Shell Rock River

Biocriteria:

Upper CL: 54


Lower CL: 36


BenInsect‐TolTXPct trophic positive Relative abundance (%) of taxa that are benthic insectivores (excludes tolerant species)


MA<2Pct reproductive negative Relative abundance (%) of early‐maturing individuals (female mature age <=2 years)

SensitiveTXPct tolerance positive Relative abundance (%) of taxa that are sensitive

SLvd life history negative Taxa richness of short‐lived species

TolTXPct tolerance negative Relative abundance (%) of taxa that are tolerant

TolPct tolerance negative Relative abundance (%) of individuals that are tolerant

DomTwoPct dominance negative Combined relative abundance of two most abundant taxa


4

Southern Headwaters


Small, moderate to high‐gradient warm/coolwater streams in southern MN and the far‐western

portion of the Red River Basin


watershed area is less than 30 square miles and gradient is greater than 0.5 m/km.

Examples:

Cobb Creek, Otter Creek, Pine Island Creek, Milliken Creek, Little Cottonwood River, Okabena

Creek, Chaska Creek

Biocriteria:

Upper CL: 58


Lower CL: 44



GeneralTXPct trophic negative Relative abundance (%) of taxa that are generalist feeders

Sensitive tolerance positive Taxa richness of sensitive species

SLvdPct life history negative Relative abundance (%) of individuals that are short‐lived

SSpnPct reproductive negative Relative abundance (%) of individuals that are serial spawners (multiple times per year)

VtolTXPct tolerance negative Relative abundance (%) of taxa that are very tolerant


5

Southern Coldwater


Coldwater streams in southern MN and the far‐western portion of the Red River Basin

Examples:

South Fork of Root River, Trout Run, Vermillion River, Valley Creek, Hemingway Creek

Biocriteria:

Upper CL: 58


Lower CL: 32


CWSensitivePct_10DrgArea tolerance positive Relative abundance (%) of individuals that are sensitive in coldwater streams (scoring adjusted for drainage area)

CWTol_10DrgArea tolerance negative Taxa richness of tolerant species in coldwater streams (scoring adjusted for drainage area)

NativeColdTXPct_10DrgArea habitat positive Relative abundance (%) of taxa that are native coldwater species (scoring adjusted for drainage area)

NativeColdPct habitat positive Relative abundance (%) of individuals that are native coldwater species

HerbvPct trophic negative Relative abundance (%) of individuals that are herbivorous

SdetTXPct_10DrgArea trophic negative Relative abundance (%) of individuals that are detritivorous (scoring adjusted for drainage area)

PioneerPct life history negative Relative abundance (%) of individuals that are pioneer species


11

Classification Key for F‐IBI Applicable to Minnesota’s Streams and Rivers 1a. Northern…………..5 1b. Southern…………..2 Southern 2a. coldwater………………..Southern Coldwater (pg 5) 2b. warmwater……………..3

3a. Drainage area >300 sq mi………………….Southern Rivers (pg 2) 3b. Drainage area <300 sq mi………………….4 4a. Drainage area >30 sq mi…………... Southern Streams (pg 3) 4b. Drainage area <30 sq mi……………5 5a. Gradient >0.50 m/km…………Southern Headwaters (pg 4) 5b. Gradient <0.50 m/km…………Low‐Gradient (pg 10) Northern 5a. coldwater………………Northern Coldwater (pg 9) 5b. warmwater……………6

6a. Basin = Red…………..7 6b. Basin = other……........8 7a. Drainage area >350 sq mi………………………Northern Rivers (pg 6) 7b. Drainage area <350 sq mi………………………9

8a. Drainage area >500 sq mi………………Northern Rivers (pg 6) 8b. Drainage area <500 sq mi………………9

9a. Drainage area >50……………....Northern Streams (pg 7) 9b. Drainage area <50………………10 10a. Gradient >0.50 m/km…...Northern Headwaters (pg 8)

10b. Gradient <0.50 m/km…...Low‐Gradient (pg 10)

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