_Policy 10-1_Appendices.pdf

Aquatic Life Use Attainment

Methodology to Determine Use Attainment for

Rivers and Streams

Policy Statement 10-1

Colorado Department of Public Health and Environment Water Quality Control Commission

4300 Cherry Creek Dr. South Denver Colorado 80246-1530

Approved: August 7, 2017 Expires: December 31, 2020

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Table of Contents

I. INTRODUCTION

II. COLORADO’S AQUATIC LIFE USES

III. BACKGROUND

IV. BIOASSESSMENT AND BIOLOGICAL THRESHOLDS

V. METHODOLOGY FOR DETERMINING CURRENT

BIOLOGICAL CONDITION

VI. HISTORY OF USE ATTAINMENT DECISIONS BASED ON

BIOLOGICAL INFORMATION

VII. ASSOCIATION BETWEEN AQUATIC LIFE POLICY AND OTHER

WQCC ACTIONS…………………………………………………………………7

VIII. AQUATIC LIFE USE ATTAINMENT: BASIC CONCEPTS

IX. AQUATIC LIFE USE ATTAINMENT: NUMERICAL THRESHOLDS

X. REFERENCES……………………………………………………………………14

XI. APPENDICES

A. MMI FINAL REPORT - RECALIBRATION OF THE COLORADO

MACROINVERTEBRATE MULTI-METRIC INDEX FOR 2017

B. BENTHIC MACROINVERTEBRATE SAMPLING STANDARD OPERATING

PROCEDURES

C. STANDARD OPERATING PROCEDURES FOR LABORATORY

IDENTIFICATION AND ENUMERATION

D. METHODOLOGY FOR DETERMINING BIOLOGICAL CONDITION

E. THRESHOLD DEVELOPMENT - TECHNICAL UNDERPINNINGS

F. BIG RIVER ANALYSIS – DATA AND GRAPHS

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List of Tables

Table 1 Aquatic Life Use Thresholds Table 2 Auxiliary Metric Thresholds for Class 1 Waters with MMI

Scores Between the Attainment and Impairment Thresholds Table 3 Criteria for Protection of High Scoring Waters

List of Figures

Figure 1 Flowchart: Comparison with Aquatic Life Thresholds Figure 2 Flowchart: Protection of High Scoring Waters

List of Acronyms and Abbreviations

AAH Administrative Action Hearing

Commission Colorado Water Quality Control Commission

CPW Colorado Parks and Wildlife (formerly known as Colorado Division of Wildlife or CDOW)

CWQCA Colorado Water Quality Control Act

CWA Clean Water Act

Division Colorado Water Quality Control Division

EPA U.S. Environmental Protection Agency

EPT Taxa The number of Ephemeroptera, Plecoptera and Trichoptera genera represented in a macroinvertebrate sample. These genera are generally very sensitive to pollution.

mi2 Square mile

MMI Multi-metric Index

WQCC Water Quality Control Commission

WQCD Water Quality Control Division iii

Definitions

Aquatic Assemblage means a group of interacting species in a given water body, united by habitat and ecology. For example, “fish assemblage” or “benthic macroinvertebrate assemblage.”

Benthic Macroinvertebrates (also macrobenthos) means the animals (without backbones) living on or in the streambed. These animals generally are large enough to be seen by the unaided eye; the size of the smallest organisms in this community is determined operationally by what can be retained by a U.S. Standard No. 30 sieve (28 openings/inch, 0.595-mm openings).

Big Rivers are considered major rivers with a cumulative watershed area exceeding 2700 mi2.

Biological Assessment (or bioassessment) means an evaluation of the biological condition of a water body using biological survey data and other direct measurements of resident biota in surface waters.

Biological Thresholds means numeric values or narrative expressions that describe the expected biological quality of aquatic communities in waters of a given classified aquatic life use. Biological thresholds are based on direct measurement of the aquatic community, including its structure and functions.

Gray Zone means that the biological condition is neither impaired nor in attainment of the use based on Interval and Equivalence tests in which neither hypothesis is rejected. More information, in the form of two auxiliary metrics, are considered before reaching a conclusion about impairment for Class 1 waterbodies.

Metric means a calculated term or enumeration representing some aspect of biological assemblage, function, or other measurable aspect. A multimetric approach combines metrics to provide an integrative assessment of the status of aquatic resources.

AQUATIC LIFE USE ATTAINMENT

METHODOLOGY TO DETERMINE USE ATTAINMENT

FOR RIVERS AND STREAMS

I. INTRODUCTION

Direct measurement and characterization of the health and well-being of the aquatic community in surface water are critical to determining how effectively Colorado is achieving the ultimate goals of the Colorado Water Quality Control Act (“CWQCA”) and the Federal Clean Water Act (“CWA”), which are to restore, maintain, protect, and improve the quality of our water resources.1 To this end, one of the specific policy goals of the CWQCA is the “protection and propagation of wildlife and aquatic life.2” The Federal CWA similarly speaks to the importance of healthy aquatic ecosystems in its often-quoted Congressional declaration, which sets forth the CWA’s key objective - to “restore and maintain the chemical, physical and biological integrity of the Nation’s waters.3” These legislative policy statements highlight the importance of having tools and techniques available to evaluate the current aquatic-life conditions in our surface waters, and to set goals for the future.

This policy document provides the Colorado Water Quality Control Commission’s (“commission”) methodology for determining whether the aquatic life use is attained in rivers and streams. The procedures detailed in this guidance rely upon direct measurement of the aquatic life use rather than on comparing existing water quality to numeric standards for individual pollutants (e.g. copper, zinc, ammonia) set to protect aquatic life.

The commission’s approach to making aquatic life use-attainment decisions has evolved over time. The intent of this policy is to describe the cumulative result of regulatory actions taken by the commission. It is envisioned that as the commission gains experience and takes action on individual use-attainment decisions in the context of Regulation No. 93 “Colorado’s Section 303(d) List of Impaired Waters and Monitoring and Evaluation List” and in considering re-classification of water bodies in rulemaking hearings, this policy document will be revised to reflect those new policy decisions.

The contents of this document have no regulatory effect, serving instead to summarize the commission’s thinking and actions in a single public document. In other words, as opposed to a rule or regulation, this policy statement has no binding effect on the commission, the Water Quality Control Division ("division"), or the regulated community. Moreover, this policy is not intended, and should not be interpreted, to limit any options that may be considered or adopted by the commission in future rulemaking proceedings. Therefore, this policy statement can, and will, be modified over time as warranted by future rulemaking decisions.

II. COLORADO’S AQUATIC LIFE USES

Colorado classifies water bodies for beneficial uses that, along with chemical and physical standards, assure their protection. Colorado has four classifications for waters: water supply, 1 See Colorado Water Quality Control Act, § 25-8-102(2), C.R.S.; Federal Clean Water Act, § 101(a), 33 U.S.C.

§ 1251(a).

2 Colorado Water Quality Control Act at section 25-8-101(2) and Clean Water Act at section 101(a) (2).

3 Federal Clean Water Act at section 101(a), emphasis added.

recreation, agriculture and aquatic life. Colorado’s aquatic life use classifications are assigned to individual water body segments based upon the potential to support that use according to a narrative description in Regulation No. 31 “Basic Standards and Methodologies for Surface Water” at section 31.13:

31.13 STATE USE CLASSIFICATIONS

Waters are classified according to the uses for which they are presently suitable or intended to become suitable. In addition to the classifications, one or more of the qualifying designations described in section 31.13(2), may be appended. Classifications may be established for any state surface waters, except that water in ditches and other manmade conveyance structures shall not be classified.

(1) Classifications

(c) Aquatic Life These surface waters presently support aquatic life uses as described below, or such uses may reasonably be expected in the future due to the suitability of present conditions, or the waters are intended to become suitable for such uses as a goal:

(i) Class I - Cold Water Aquatic Life These are waters that (1) currently are capable of sustaining a wide variety of cold water biota, including sensitive species, or (2) could sustain such biota but for correctable water quality conditions. Waters shall be considered capable of sustaining such biota where physical habitat, water flows or levels, and water quality conditions result in no substantial impairment of the abundance and diversity of species.

(ii) Class 1 - Warm Water Aquatic Life These are waters that (1) currently are capable of sustaining a wide variety of warm water biota, including sensitive species, or (2) could sustain such biota but for correctable water quality conditions. Waters shall be considered capable of sustaining such biota where physical habitat, water flows or levels, and water quality conditions result in no substantial impairment of the abundance and diversity of specifies.

(iii) Class 2- Cold and Warm Water Aquatic Life These are waters that are not capable of sustaining a wide variety of cold or warm water biota, including sensitive species, due to physical habitat, water flows or levels, or uncorrectable water quality conditions that result in substantial impairment of the abundance and diversity of species.

III. BACKGROUND

Historically, Colorado’s aquatic life use classifications have sometimes been difficult to determine for a given water body. The broad categories and the generalized terms in the classification descriptions have led to disagreements and sometimes contentious hearings about the appropriate classification of specific water bodies.

The current effort to refine the aquatic life use classifications and provide a more consistent basis for determining the condition of aquatic life arose from specific issues in Colorado, as well as an increased national focus on biological thresholds. In the late 1990’s, a contentious hearing about the proper classification of the Lower Arkansas River raised awareness of problems with the existing descriptions of the aquatic life use classifications. This coincided with EPA encouragement for States to incorporate biological assessments and biological thresholds as major components of their monitoring and assessment programs. In June 2000, the division established the Aquatic Life Work Group to develop biological assessment methods and biological thresholds, and propose refinements of the aquatic life use classifications.

In 2002, an amendment of the CWQCA (§ 25-8-309) directed the division to study (among other things) the need for refined aquatic life use classifications and a better method with a uniform approach to determine whether a water body had attained its aquatic life use. These subjects were explored by the Aquatic Life Work Group. The result of the CWA Section “309” study was to flesh out the expected condition concept and identify a “Strawman” classification system which contained nine primary aquatic life use categories and 27 possible subcategories and called for voluntary pilot studies to characterize the “expected condition” for candidate sub-categories. However, the pilot studies did not proceed as intended due to a lack of interest, funding, and study sites.

In November of 2004, the commission reviewed the Aquatic Life Work Group’s “expected condition concept” during the Basic Standards Issues Formulation Hearing. At that time, the commission decided not to incorporate the expected condition concept in the 2005 Basic Standards and Methodologies for Surface Water (Regulation #31) Rulemaking Hearing.

Instead, the commission tasked the Aquatic Life Work Group with strengthening the underlying biological data from which the Strawman’s nine principle use classification categories and sub-classifications would be defined. At that time the commission targeted the 2010 Rulemaking Hearing for Basic Standards for the next Strawman iteration.

Coincidentally, the division began to work with the EPA and their contractors to use Colorado’s data to develop bioassessment tools. This effort is described below in Section IV.

Rather than restructuring the existing classification system with potentially numerous ramifications, the division decided to proceed with the more modest step of utilizing bioassessment tools and data to refine how existing classifications are interpreted and applied. This policy represents the first official step to add more specificity to Colorado’s aquatic life use classifications.

IV. BIOASSESSMENT AND BIOLOGICAL THRESHOLDS

Bioassessment is a quantitative measure of the biological condition of the resident aquatic community. A biological threshold is the establishment of numeric criteria against which the current biological condition can be evaluated. Each of these regulatory concepts – biological assessment and biological thresholds – are defined briefly in the Definitions section, and then discussed in more detail in Section IV subsection A.

A. Bioassessment Tools

Aquatic communities are an association of interacting populations of aquatic organisms in a given waterbody or habitat (EPA 1991). They provide valuable information regarding the overall biological integrity of a given waterbody. These organisms are capable of integrating the effects of stressors over time; thus, they can provide a broad ecological measure of fluctuating environmental conditions (EPA 1999). Bioassessments provide the means to evaluate biological condition in relation to the goal or expectation, such as designated use support.

Several biological assemblages are available for study including periphyton (attached algae), benthic macroinvertebrates and fish, each of which responds somewhat differently to the suite of anthropogenic stressors. The decision to rely exclusively on the benthic macroinvertebrates assemblage was based on community characteristics and practical considerations. The combination of short life spans, limited migration patterns, representation in most Colorado habitats, and ease of collection make macroinvertebrates the best single assemblage for bioassessment.

Within the benthic macroinvertebrate assemblage, metrics are selected that represent some measureable aspect of the community structure and function. These measurements are grouped into five metric categories: taxa richness, composition, pollution tolerance, functional feeding groups, and habit (mode of locomotion). Combining metrics from these categories into a multi-metric index transforms taxonomic identifications and individual counts into a unitless score that ranges from 0-100.

Choosing metrics that are sensitive to stressors yields an index that defines the health, or the biological condition, of the aquatic community. A bioassessment tool of this kind is a powerful basis for a direct assessment of aquatic communities that can be used to reach conclusions about attainment of the aquatic life use.

B. Colorado’s Multi-Metric Index (MMI) Bioassessment Tool

The division, with assistance from EPA and its contractors, has developed a multi-metric bioassessment tool for Colorado that is composed of separate indices calibrated to respond to stressors affecting aquatic communities in one of the three analytically defined Biotypes.4

Multi-metric indices were then calibrated for each Biotype. Each index is composed of several metrics selected to represent categories of community characteristics including richness, composition, functional feeding group, habit (mode of locomotion), and pollution tolerance. Metrics were chosen on the basis of their ability to discriminate between reference and stressed sites, represent multiple metric categories, are ecologically meaningful, and are not redundant with other metrics in the index. See Appendix A for details.

Because of this metric selection process, the metrics used in the MMI vary in their ability to detect or diagnose specific types of stress. The MMI is designed to detect environmental stresses that result in alteration of the biological community. No specific stressors are identified because the intent is to have a generalized tool that responds to a wide range of potential stressors. In other words, the MMI tool cannot determine if the stressor is a specific pollutant, pollution or habitat limitation (including flow). Once impairment is identified, however, other tools are available to identify the likely cause of impairment.

4 A Biotype is an aggregation of macrobenthos sites that have similar community composition. Environmental attributes (elevation, stream slope and ecoregion) common to sites within each of the Biotypes can be used to predict membership of a new site.

V. METHODOLOGY FOR DETERMINING CURRENT BIOLOGICAL CONDITION

Determining biological condition involves the steps of calculating the MMI for the appropriate Biotype and comparing the MMI score to a threshold.

To calculate an MMI a representative macroinvertebrate sample is collected from the appropriate habitat(s). Standardized procedures for collecting macroinvertebrates are in Appendix B. Field sampling is typically followed by preservation, laboratory identification and enumeration, and entry into a biological database capable of calculating the MMI. See Appendices C and D for details.

VI. HISTORY OF USE ATTAINMENT DECISIONS BASED ON BIOLOGICAL

INFORMATION

Direct measurement and characterization of the health and well-being of the aquatic community in surface water is critical to determine whether or not the aquatic life use is attained at a given site. Historically, Colorado has used biological information to make attainment decisions, even though no specific methods of assessment or thresholds were set.

This section describes the history of such decisions.

A. Impaired Waters Listing Decisions

In 1998, the Colorado List of Impaired Waters included three segments found to be impaired for aquatic life. The associated listing methodology explained the protocol for reaching those decisions:

Biological assessments by the Colorado Division of Wildlife (CDOW) were utilized in developing the List. These consist of fish surveys performed by CDOW staff using both seining and electrofishing. The results of these assessments were compared with the Standards and Classification System in the following manner. For segments that are designated as Aquatic Life Class 1, evidence of a decline over time from a healthy and diverse fish community or the absence of a Species of Critical Concern5 constitutes an impairment of the use. For segments that are designated as Aquatic Life Class 2, evidence of significant reduction of the species composition of a fish community over time constitutes an impairment of the use. The Division limited the time frame for comparison of fish communities as shown by fish surveys, to only the late 1970’s (when aquatic life classes were established) through more recent conditions.

The requirement for a Section 303(d) List in 2000 was suspended by EPA, and no List of Impaired Waters was compiled. The 2002 303(d) List included six waters with an impaired aquatic life use. Decisions about impairment were based on the following narrative that appeared in the 2002 Listing Methodology:

B. IMPAIRMENT OF NARRATIVE STANDARDS AND CLASSIFIED USES

Impairment of narrative standards and classified uses may be supported by chemical data and/or information generated by biological and/or physical assessments. In

5 Species of Critical Concern includes native fish species observed to be in decline and rare in abundance or limited in distribution (as identified by CPW in the Inventory and Status of South Platte River Native Fishes in Colorado, CPW, 1997).

instances where a determination of impairment is based solely upon biological and/or physical assessments, such assessments must provide clear and convincing evidence of non-attainment. For aquatic life uses, as previously referenced, the WQCD will generally consider impairment of narrative standards and classified uses to be demonstrated when either the physical/habitat data or biological community metrics reflect a condition that is significantly less than reference condition. When such data do not indicate specific pollutant(s) causing non-attainment, the WQCD may place the segment on the M&E List for further study.

In 2004, the Section 303(d) List was promulgated as Regulation No. 93, and the Monitoring and Evaluation List became Regulation No. 94. As in 2002, a separate Listing Methodology document was developed. The 2004 Section 303(d) List included six waters with an impaired aquatic life use. The 2004 Listing Methodology section regarding decisions of impairment based on biological information is essentially the same as 2002, but with the addition of the concept of “expected condition,” as provided below.

3. Impairment of Narrative Standards and Classified Uses data and/or information generated by biological and/or physical assessments. In instances where a determination of impairment is based solely upon biological and/or physical assessments, such assessments must provide clear and convincing evidence of non-attainment. For aquatic life uses, as previously referenced, the Division will generally consider impairment of narrative standards and classified uses to be demonstrated when either the physical/habitat data or biological community metrics reflect a condition that is significantly less than the expected or reference condition.

When such data do not indicate specific pollutant(s) causing non-attainment, the Division will recommend placing the segment on the M&E List for further study. (emphasis added).

The 2006 Section 303(d) List included three segments determined to be impaired for the aquatic life use. The 2006 Listing Methodology considerations were the same as 2004. In 2008, the structure of this portion of the Listing Methodology was modified;

however, the level of proof (clear and convincing) and decline from reference condition (significantly less than) remained unchanged. The 2008 Section 303(d) List contained four segments with aquatic life use impairment (not including Fish Consumption Advisories). The 2008 Listing Methodology explained as follows:

3. Impairment of Narrative Standards and Classified Uses data and/or information generated by biological and/or physical assessments. In instances where a determination of impairment is based solely upon biological and/or physical assessments, such assessments must provide clear and convincing evidence of non-attainment.

a. Aquatic Life Use: For aquatic life uses, as previously referenced, the Division will generally consider impairment of narrative standards and classified uses to be demonstrated when either the physical/habitat data or biological community metrics reflect a condition that is significantly less than the expected or reference condition.

The 2010 Section 303(d) List contained three segments for aquatic life use impairment (not including Fish Consumption Advisories). The 2010 Listing Methodology has the same provisions as the 2008 Methodology; however, Regulation Nos. 93 and 94 were combined as Regulation No. 93.

The 2012 Section 303(d) List contained 33 segments for aquatic life use impairment.

Four segments were fully listed, meaning a pollutant was identified. Twenty-nine segments were provisionally listed, meaning a pollutant was not identified. 303(d) priority for provisionally listed segments ranged from low to high in some cases although most tended to be prioritized as “low”. Twenty-two segments or portions of segments were placed on the Monitoring and Evaluation List. The division integrated sites within these segments into subsequent monitoring plans to be sampled.

The 2014 Section 303(d) List was not completed due to a re-prioritization of resources in the division.

The 2016 Section 303(d) List contained 81 segments for aquatic life use impairment.

Sixteen segments were fully listed, meaning a pollutant was identified. Fifty segments were provisionally listed, meaning a pollutant was not identified. Fifteen segment or portions of segments were placed on the Monitoring and Evaluation List. The division integrated sites within these segments into subsequent monitoring plans to be sampled.

VII. ASSOCIATION BETWEEN AQUATIC LIFE POLICY AND OTHER WQCC ACTIONS

Aquatic Life Use Policy 10-1 provides guidance for determining whether sites on rivers and streams with watersheds less than 2700 square miles and big rivers on the Western Slope of Colorado are attaining their aquatic life use. It offers a systematic assessment method for comparing the biological condition of a test site in a given Biotype, as characterized by an MMI score, against an expectation of biological condition (threshold) for a similar Biotype. If biological conditions fall below expectations, the site may be deemed “impaired”.

Once a determination of impairment is reached, there is a range of possible regulatory outcomes that may be reached. One outcome is inclusion in the biennial Regulation No. 93 “Colorado’s Section 303(d) List of Impaired Waters and Monitoring and Evaluation List”.

Another is through the consideration of re-classification of water bodies in rulemaking hearings. These commission actions are guided by their own policy considerations, which should be consulted separately as the need arises.

It is envisioned that as the commission gains experience and takes action on individual use-attainment decisions in these or other contexts, this policy document will be revised to reflect those evolving policy decisions. Further, if major changes are made in related policy documents, (i.e., the section regarding “Impairments where the Pollutant is Unknown” in the Section 303(d) Listing Methodology), those policy changes may necessitate changes to Aquatic Life Use Policy 10-1.

VIII. AQUATIC LIFE USE ATTAINMENT: BASIC CONCEPTS

In order to protect and maintain Colorado’s aquatic life, it is the policy of the commission to apply a defined method and a uniform approach to determine whether a water body has attained its aquatic life use classification. The method and approach are based on the following tenets:

1. Quantitative Assessment of the Biological Condition: The commission has determined that the Colorado Multi-Metric Index is an appropriate tool for quantitative bioassessment because:

• The condition of the macroinvertebrate community is an appropriate surrogate for the entire aquatic community.

• The macroinvertebrate community is an appropriate indicator of stream quality because of limited migration patterns and short life spans. As such, they are capable of integrating the effects of physical and chemical stressors over short time periods (weeks to months).

• The Multi-Metric Index tool and subsequent iterations were developed exclusively with macroinvertebrate data collected in Colorado.

• Supporting data represent the variability expected within the State and accounts for the broad environmental gradients through spatial classification.

2. Comparison with Expected Condition: The commission continues to support the use of “reference condition” or “expected condition” as the basis for characterizing use support. It is important to note that this concept of use support embraces considerable variation in the biological community. This variability must be acknowledged in developing the biological thresholds and implementation approach.

3. Impairment is a Significant Departure from Expected Condition: At this time, the commission affirms the position taken in prior decisions made in the context of the Section 303(d) Listing Methodology - that clear and convincing evidence is needed to show impairment, and that the status of non-attainment represents a significant departure from reference or expected condition.

4. Recognition of Warm / Cold Distinction: The commission believes it is important to preserve the existing distinction between warm-water and cold-water biota that is set forth in the Basic Standards. Accordingly, the assessment methodology should accommodate the different thermal tolerances that are expected within each subclass.

5. Recognition of Class 1 / Class 2 Distinction: The commission believes it is important to preserve the existing distinction between Class 1 and Class 2 aquatic life classifications that is set forth in the Basic Standards, i.e. that Class 1 waters are to be capable of sustaining a wide variety of biota including sensitive species.6 Accordingly, showing attainment of the Class 1 aquatic life use may require additional demonstration that diversity and sensitivity characteristics are maintained.

6. Statistical Methods: Consistent with CWQCA at section 25-8-204(5), the commission requires that statistical methodologies be based on assumptions that are compatible with the water quality data. Application of those methodologies should be transparent with respect to uncertainty and risk of mistaken conclusions.

6 Regulation No. 31, section 31.13(1)(c)(i).

7. Protection Against Large Decline: Natural variability in biological condition at reference sites leads to thresholds that could inadvertently expose high scoring sites to the risk of undetected degradation. It is the commission’s policy to provide additional protection by defining an allowable change in biological condition that is independent of biological thresholds.

IX. AQUATIC LIFE USE ATTAINMENT: NUMERICAL THRESHOLDS

It is the commission’s intent that there should be predictable, transparent, and understandable techniques for evaluating the aquatic life use, and that the methods for assessing attainment of the aquatic life use should be consistent with the classifications and standards system previously adopted by the commission.

A. Use Attainment Thresholds for Streams and Small Rivers

For Colorado’s streams and rivers with a watershed area less than 2,700 mi2 and those big river watersheds listed in Section IX subsection B, the commission has established aquatic life use attainment thresholds that were derived using a statistical methodology that relies on a normal operating range to define use support and interval and equivalence tests.

1. Quantitative Assessment of Biological Condition: Implementation of this policy relies upon use of the Colorado MMI (version 4, 2017, see Appendix A). The following documents describe the procedures for collecting data and determining MMI scores:

• Benthic Macroinvertebrate Sampling Standard Operating Procedures (Appendix B)

• Standard Operating Procedures for Laboratory Identification and Enumeration (Appendix C)

• Methodology for Determining Biological Condition (Appendix D)

2. Recognition of Warm / Cold Distinction: Use of the predictor variables for establishing Biotype membership provides appropriate refined recognition of the thermal tolerances that are expected within the warm water and cold water biota subclasses. Sites are to be compared against the attainment and impairment thresholds for their predicted Biotype.

3. Comparison with Aquatic Life Thresholds: Thresholds are established based on analysis of the biological condition at reference sites in each of three Biotypes. Figure 1 provides a flowchart of the comparison process. Derivation of thresholds is described in Appendix E.

Table 1. Aquatic Life Use Thresholds Biotype Attainment

Threshold Impairment Threshold

1 Transition 45 34 2 Mountains 48 40 3 Plains & Xeric 42 29

• Class 1 water bodies: An MMI score in the gray zone for a site on a Class 1 water requires examination of additional information – see Subsection 4 below.

• Class 2 water bodies: When the MMI score falls within the gray zone (between the attainment and impairment thresholds discussed above) and the site is from a Class 2 stream, the stream is considered to be in support of the use.

Figure 1. Flowchart: Comparison with Aquatic Life Thresholds

4. Recognition of Class 1 / Class 2 Distinction: The Hilsenhoff Biotic Index and the Shannon Diversity Index are used as auxiliary metrics that supplement the MMI for Class 1 waters with MMI scores between the attainment and impairment thresholds. If a Class 1 site fails to meet the criteria shown in Table 2 for either auxiliary metric, the site will be considered impaired. For Class 2 waters, the premise that these “waters are not capable of sustaining a wide variety of cold or warm biota, including sensitive species” mitigates the need to further confirm attainment or impairment through use of auxiliary metrics. Accordingly, for Class 2 waters, a single threshold provides the basic determinant between attainment and impairment (see Table 1). Auxiliary metrics are not applicable to Class 2 waters. Derivation of Auxiliary Metric thresholds is described in Appendix E.

Table 2. Auxiliary Metric Thresholds

For Class 1 Waters with MMI Scores Between the Attainment and Impairment Thresholds

Biotype Hilsenhoff Biotic Index

Shannon Diversity Index

1 Transition <5.8 >2.1 2 Mountains <4.9 >3.2 3 Plains & Xeric <7.6 >2.4

5. Protection Against a Large Decline: Thresholds are established for a decline in biological condition that is acceptable over time. Samples must be representative of normal conditions and be separated by more than 12 months. Conditions under which factors of representativeness apply may be found in Section IX, subsection C of this document. Table 3 presents the thresholds for “high scoring waters7” for each Biotype. More than a 22 point decline in the MMI score results in a conclusion of impairment. Figure 2 provides a flowchart for determining protection of high scoring waters. Derivation of High Scoring Waters thresholds is described in Appendix E.

Table 3. Criteria for Protection of High Scoring Waters 7

Biotype High Scoring Water (MMI score)

Allowable MMI decline

1 Transition >56 -22 2 Mountains >62 -22 3 Plains & Xeric >51 -22

7 In concept, this threshold applies to all sites; in practice, it affects only high-scoring sites since a large decline for a moderate scoring site would bring it below the attainment threshold. The MMI threshold that constitutes a high score is indicated in Table 3.

B. Use Attainment Thresholds for Big Rivers:

The commission will apply the 2017 MMI-based Impairment Thresholds to watershed areas >2,700 mi2 in the Yampa River, White River, Colorado River, Gunnison River, Dolores River, and San Juan River basins. Cluster analysis has demonstrated that the benthic macroinvertebrate composition, as defined by common genus taxonomy, in those bigger rivers are statistically comparable to the benthic macroinvertebrate compositions in smaller sized tributaries within the same basins. See Appendix F for data used in this analysis.

The commission will continue not to apply the 2017 MMI-based Impairment Threshold to watershed areas >2,700 mi2 in the South Platte River, Arkansas River, including the Purgatoire River, and Rio Grande River basins.

C. Considerations of Representative Data

The 2016 Section 303(d) Listing Methodology contains appropriate coverage of the representative data issue: It clearly provides: “Data that are not representative of normal conditions shall typically be discounted in making the listing decision.” The

Figure 2. Flowchart: Protection of High Scoring Waters

2016 Listing Methodology explains “representativeness” as follows: “[T]he Monitoring and Evaluation List identifies water bodies where there is reason to suspect water quality problems, but there is also uncertainty regarding one or more factors, such as the representative nature of the data.”

1. The representativeness of an individual sample may be affected by antecedent physical or chemical events within the generation time of the macroinvertebrate community. Events might include seasonal water level fluctuations that may dry/wet a portion of the targeted sampling habitat, scouring flood flows or accidental spills of toxic chemicals.

2. The representativeness of an individual sample may be inferred from spatial or temporal patterns where multiple samples exist. For example, an anomalously low MMI score at one site in a spatial group or on one date in a time series might be evidence that a site is not representative. Therefore, it is important to ensure that samples are collected from habitat with similar depth/substrate/velocity conditions to minimize the potential effect of sampling bias. Furthermore, there must be no evidence of perturbation that could explain the low score.

3. The length of stream that a single sample can fairly represent depends on the site-specific considerations of the location. Generally, the length would be limited to a portion that was hydrologically consistent with the sample location (i.e., no intervening dams, diversions, tributaries or discharges). It is also important to consider the potential change from perennial to seasonally intermittent/ephemeral flow conditions within the segment, especially during alternating dry/wet year type conditions.

D. Alternative Thresholds

In order to set an alternative threshold, a party would need to establish that the situation is “natural or man-induced irreversible” (i.e., there are no sources to remediate) and determine the central tendency of the MMI scores. The mechanism for establishing alternate methodologies for assessing the biological condition against the expected condition is best defined through the Regulation No. 93 Section 303(d) Listing Methodology, which is updated biennially.

X. REFERENCES

Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling. 1999. Rapid Bioassessment

Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish, Second Edition. EPA 841-B-99-002. U.S. Environmental Protection Agency; Office of Water; Washington, D.C.

Colorado Division of Wildlife, 1997. Inventory and Status of South Platte River Native Fishes in Colorado.

U.S. Environmental Protection Agency. 1991. Biological Criteria: State Development and

Implementation Efforts. EPA 440-5-91-003. Office of Water; Washington, D.C.

APPENDIX A

MMI FINAL REPORT

Recalibration of the Colorado Benthic Macroinvertebrate Multimetric Index

Prepared for:

Colorado Department of Public Health and Environment Water Quality Control Division – Environmental Data Unit

Prepared by:

Benjamin K. Jessup1 and James B. Stribling2

Tetra Tech, Inc.

Center for Ecological Sciences

173 Main Street, Suite 38 Montpelier, VT 05602 and 210711 Red Run Boulevard, Suite 105

Owings Mills, MD 21117

Final Report April 25, 2017

Colorado Macroinvertebrate Index Development April 25, 2017

Tetra Tech, Inc. i

Abstract

The Colorado Department of Public Health and Environment (CDPHE) monitors streams throughout the state for assessment and protection of water resource quality. Their principal indicator is a multimetric index (MMI) which is based on direct benthic macroinvertebrate sample data collected from each waterbody. As a quantitative descriptor of stream conditions, the MMI and its components can be associated with known environmental gradients, both natural and those resulting from human disturbance. Prior index calibration in 2008 identified gradients related to natural conditions, and within them recognized three distinct sites classes as biological types, generally related to sites in the mountains (Biotype 2), plains (Biotype 3), and transitional regions (Biotype 1). Within each Biotype, variability was quantified and partitioned by adjusting metrics relative to factors such as summer temperature, elevation, and sample date. The purpose of this project is to recalibrate the Colorado MMI with sample data from 601 additional stream sites collected since 2008, and an expanded understanding of statewide stream characteristics. Defining responsiveness and robustness of metrics as those that, respectively, exhibit detectable change in the presence of stressors, and that represent diverse sample characteristics, we evaluated 104 metrics. Responsiveness of more than 150,000 index alternatives per Biotype were tested for their ability to detect differences between reference and stressor sites. Three separate indices, one for each Biotype, were selected, are comprised of eight metrics, and have a cumulative capacity for correctly distinguishing reference from stressed condition (discrimination efficiency [DE]) 97.1 percent of the time.

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Table of Contents Abstract ................................................................................................................................ i Table of Contents ............................................................................................................... iii List of Tables ..................................................................................................................... iv List of Figures ..................................................................................................................... v 1 Introduction

Clean Water Act 2 Data Description 3 Analytical Methods

3.1 Site Classification

Biological Groupings Discerning Environmental Factors Site Classes

3.2 Metric Calculations

Metric Descriptions Indicator taxa Metric adjustment to environmental conditions Metric Evaluation

3.3 Index Composition

Metric Scoring Index Composition Metric and Index Precision

4 Results

4.1 Site Classification

Ordination Cluster Analysis Metric and Environmental Variable Distributions Discriminant Analysis CART and Random Forest Analysis Site Classification Conclusions

4.2 Metric Development

Indicator Taxa Metrics Adjustments to Environmental Variables Metric Performance

4.3 Index Performance

Biotype 1 Biotype 2 Biotype 3

4.4 Index Application

5 Conclusions and Recommendations 6 References Cited

Appendices A Reference and Stressed Sites used in Analysis B Metric Adjustments C Metric Performance

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List of Tables

Table 1. Reference and stressed site tally by ecoregion Table 2. Data treatments for consistency in analysis Table 3. Predictor variables listed categorically. This list does not include all the possible variations of each variable, which included statistical summaries by watershed or at the sampling point Table 4. Metric descriptions Table 5. Variables tested for metric adjustments Table 6. Site Classification Rules Table 7. Random Forest importance of environmental variables in predicting reference PA clusters Table 8. Indicator taxa derived from an indicator species analysis on reference and stressed sites Table 9. Mid-elevation sensitive and tolerant families Table 10. Metrics included in the Biotype 1 MMI with scoring formulae Table 11. The best index alternatives considered for Biotype 1, including eight that resulted from screening the all-subsets models, the best manually derived model, and the metrics from the existing MMI. The selected metric is #8_61382 Table 12. Precision statistics for the selected Biotype 1 index and its component metrics, based on both metric scores and values Table 13. Metrics included in the Biotype 2 MMI with scoring formulae Table 14. The best index alternatives considered for Biotype 2, including 8 that resulted from screening the all-subsets models, the best manually derived model, and the metrics from the existing MMI. The selected metric is #8_78149 Table 15. Precision statistics for the selected Biotype 2 index and its component metrics, based on both metric scores and values Table 16. Metrics included in the Biotype 3 MMI with scoring formulae Table 17. The best index alternatives considered for Biotype 3, including 8 that resulted from screening the all-subsets models, the best manually derived model, and the metrics from the existing MMI. The selected metric is #8_70028 Table 18. Precision statistics for the selected Biotype 3 index and its component metrics, based on both metric scores and values Table 19. MMI performance statistics

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List of Figures

Figure 1. Reference and stressed sites by Biotype (Group) overlaid on level 3 ecoregions in Colorado Figure 2. Typical inputs and results in a discrete classification process. Inputs include natural environmental variables and biological similarities among sites. Resulting site classes are discrete bins, where a site can be placed in only one bin Figure 3. Example diagram of metric adjustment showing optimal expectations (black dashed line) for Beck’s Biotic Index along the elevation gradient. The red line is the LOWESS regression line Figure 4. Illustration of metric discrimination efficiency (DE) between reference and stressed sites for EPT taxa in Biotype 1. The DE is between 50 and 75%, judging from the stressed metric value distribution relative to the reference 25th percentile Figure 5. Illustration of metric Z-score between reference and stressed sites for EPT taxa in Biotype 2. It appears that approximately 1.4 standard deviations of reference sites metric values fit into the gap between the reference and stressed mean values Figure 6. NMS ordination of taxa presence/absence data in 144 reference sites, showing the existing classification scheme with three Biotypes Figure 7. NMS ordination of taxa relative abundance data in 144 reference sites, showing the existing classification scheme with three Biotypes Figure 8. PCA ordination of taxa relative abundance data in 144 reference sites, showing the existing classification scheme with three Biotypes Figure 9. Cluster analysis using taxa presence/absence data from 144 reference sites, showing color-coded existing Biotypes Figure 10. Cluster analysis using taxa presence/absence data from 144 reference sites, showing color-coded Bioregions (Mountains = red, Plains = blue, Xeric = black) Figure 11. Distributions of environmental variables (catchment size, elevation, and summer air temperature) in the Biotypes Figure 12. Distributions of macroinvertebrate metrics (EPT taxa, predator + scraper taxa, and Hilsenhoff’s Biotic Index [HBI]) in the Biotypes Figure 13. CART dendrogram showing distinctions for Biotypes 3 and 2 and a split of Biotype 1 sites by longitude Figure 14. East/West divide for transitional sites (red dashed line) derived from CART analysis Figure 15. NMS ordination of reference presence/absence data, showing Biotypes 2 and 3 and western and eastern sites in Biotype 1 (transitional) Figure 16. Distributions of environmental variables (catchment size, elevation, and summer air temperature) in the CART groups, which include Biotypes 2 and 3 and western Biotype (10) and eastern Biotype 1 (11) Figure 17. Distributions of macroinvertebrate metrics (EPT taxa, predator + scraper taxa, and Hilsenhoff’s Biotic Index [HBI]) in the CART groups, which include Biotypes 2 and 3 and western Biotype (10) and eastern Biotype 1 (11)

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Figure 18. Biotypes (Groups) for the macroinvertebrate index in Colorado Figure 19. Distribution of index scores (8_61382) in reference and stressed sites in Biotype 1, showing calibration and validation data sets Figure 20. Bi-plots of index metrics that were adjusted to summer temperature in Biotype 1, including EPT taxa, percent intolerant taxa, and clinger taxa. The plots show the LOWESS regression curve (blue) and the 95th quantile regression line (dashed) with reference sites (blue dots) Figure 21. Biotype 1 index in response to the stressor gradients: % agriculture and urban land cover and the sum of reference criterion scores indicating stressed conditions Figure 22. Distribution of index scores (8_78149) in reference and stressed sites in Biotype 2, showing calibration and validation data sets Figure 23. Bi-plot of index metric (EPT taxa) that was adjusted to Julian Day in Biotype 2, showing the LOWESS regression curve (blue) and the 95th quantile regression line (dashed) with reference sites (blue dots) Figure 24. Biotype 2 index in response to the stressor gradients: % agriculture and urban land cover and the sum of reference criterion scores indicating stressed conditions Figure 25. Distribution of index scores (8_70028) in reference and stressed sites in Biotype 3, showing calibration and validation data sets Figure 26. Sprawler taxa in relation to Julian Day in Biotype 3, showing the LOWESS regression curve (blue) and the 95th quantile regression line (dashed) with reference sites (blue dots) Figure 27. Biotype 3 index in response to the stressor gradients: % agriculture and urban land cover and the sum of reference criterion scores indicating stressed conditions Figure 28. Biotype 3 index values in relation to longitude, showing reference and stressed sites

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1 Introduction

Clean Water Act The Clean Water Act of 1972 ([CWA] USGPO 1989) has as its primary objective the maintenance and restoration of “biological integrity” of the Nation’s waters, which incorporates biological, physical, and chemical quality (§101[a]). This concept of biological integrity refers to environmental conditions that are undisturbed by human activities, and that have the capacity for supporting a natural assemblage of native organisms (Frey 1977, Karr et al. 1986, Karr 1991, Steedman 1994). As such, the most accurate, comprehensive, and robust primary indicator of undisturbed conditions is one that quantitatively describes the biota inhabiting them, with measured differences taken as response to degradation. The measurable definition of biological integrity is the reference condition (Barbour et al. 1995, 1999, Stoddard et al. 2006), which is characterized using data from minimally-disturbed reference sites within a region. In responding to the CWA, CDPHE has developed water quality standards for the protection of human and ecosystem health under the Colorado Water Quality Control Act (“CWQCA”), including establishing aquatic life uses (ALU) (Policy Statement 10-1 [CDPHE 2010a]).