A Primer on Using Biological Assessments 

to Support Water Quality Management

October 2011
U.S. Environmental Protection Agency

Office of Science and Technology

Office of Water, Washington, DC

EPA 810-R-11-01

Ken Norton, Hoopa Valley Tribe

The Hoopa Valley Tribe and neighboring tribes use traditional redwood canoes for subsistence fishing 

and ceremonial purposes.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011

A Primer on Using Biological Assessments to 

Support Water Quality Management

 

Contact Information

For more information, questions, or comments about this document, please contact Susan Jackson, 

U.S. Environmental Protection Agency, at Office of Science and Technology, Office of Water, 

U.S. Environmental Protection Agency, 1200 Pennsylvania Avenue, Mail Code 4304T, Washington, DC 

20460 or by email at jackson.susank@epa.gov. 

Acknowledgements

Thank you to the following state and tribal agencies for their support with the case studies in this 

document:

Arizona Department of Environmental Quality

Connecticut Department of Environmental Protection

Grand Portage Band of Lake Superior Chippewa

Iowa Department of Natural Resources

Maine Department of Environmental Protection

Maryland Department of the Environment

Michigan Department of Environmental Quality

Minnesota Pollution Control Agency

Narragansett Bay Estuary Program

New Jersey Department of Environmental Protection

Ohio Environmental Protection Agency

Oregon Department of Environmental Quality

Pennsylvania Department of Environmental Protection

Tampa Bay Estuary Program

Utah Department of Environmental Quality

Vermont Department of Environmental Conservation

Virginia Department of Conservation and Recreation
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 ii

Acknowledgements (continued)

Thank you to the following scientists and state and tribal agencies for their support with development 

and piloting the biological assessment tools discussed in Chapter 2

Tool #1: Biological Assessment Program Evaluation (2001 – 2009)

Alabama, Arizona,

California, Connecticut, Colorado, Florida, Illinois, Indiana, Iowa, Maine, Massachusetts, Michigan, 

Minnesota, Missouri, Montana, Fort Peck Tribes (Assiniboine and Sioux), New Hampshire, New Mexico, 

Ohio, Rhode Island, Texas, Vermont, Wisconsin

Tool #2: The Biological Condition Gradient (2000–2005) 

State and Tribal Workgroup Members

Arizona Department of Environmental Quality – Patti Spindler

California Department of Fish and Game – Jim Harrington

Colorado Department of Public Health and Environment – Robert McConnell, Paul Welsh

Florida Department of Environmental Protection – Russ Frydenborg, Ellen McCarron, Nancy Ross

Idaho Department of Environmental Quality – Mike Edmondson

Kansas Department of Health and Environment – Bob Angelo, Steve Haslouer, Brett Holman

Kentucky Department for Environmental Protection – Greg Pond, Tom VanArsdall

Maine Department of Environmental Protection – David Courtemanch, Susan Davies

Maryland Department of the Environment – Joseph Beaman, Richard Eskin, George Harmon

Minnesota Pollution Control Agency – Greg Gross

Mississippi Department of Environmental Quality – Leslie Barkley, Natalie Guedon

Montana Department of Environmental Quality – Randy Apfelbeck, Rosie Sada

Nevada Division of Environmental Protection – Karen Vargas

North Carolina Department of Environment and Natural Resources – David Lenat, Trish MacPherson

Ohio Environmental Protection Agency – Jeff DeShon, Dan Dudley

Ohio River Valley Water Sanitation Commission – Erich Emery

Oregon Department of Environmental Quality – Doug Drake, Rick Hafele

Pyramid Lake Paiute Tribe – Dan Mosley

Texas Commission on Environmental Quality – Charles Bayer

Vermont Department of Environmental Conservation – Doug Burnham, Steve Fisk

Virginia Department of Environmental Quality – Alexander Barron, Larry Willis

Washington State Department of Ecology – Robert Plotnikoff

Wisconsin Department of Natural Resources – Joe Ball, Ed Emmons, Robert Masnado, Greg Searle, 

Michael Talbot, Lizhu Wang
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 iii

U.S. Environmental Protection Agency

Office of Water: Chris Faulkner, Thomas Gardner, Susan Holdsworth, Susan Jackson, Kellie Kubena, 

Douglas Norton, Christine Ruff, Robert Shippen, Treda Smith, William Swietlik

Regional (R) Offices: Peter Nolan (R1), Jim Kurtenbach (R2), Maggie Passmore (R3), Ed Decker, Jim 

Harrison, Eve Zimmerman (R4), Ed Hammer, David Pfeifer (R5), Philip Crocker, Charlie Howell (R6), Gary 

Welker (R7), Tina Laidlaw, Jill Minter (R8), Gary Wolinsky (R9), Gretchen Hayslip (R10)

Office of Environmental Information: Wayne Davis

Office of Research and Development: Karen Blocksom, Susan Cormier, Phil Larsen, Frank McCormick, 

Susan Norton, Danielle Tillman, Lester Yuan 

US Geological Survey (USGS)

Evan Hornig, Ken Lubinski

Scientific Community

David Allan, University of Michigan

Michael Barbour, Tetra Tech, Inc.

David Braun, The Nature Conservancy

Jan Ciborowski, University of Windsor

Jeroen Gerritsen, Tetra Tech, Inc.

Richard Hauer, University of Montana

Charles Hawkins, Utah State University

Bob Hughes, Oregon State University

Lucinda Johnson, University of Minnesota

James Karr, University of Washington

Dennis McIntyre, Great Lakes Environmental Center

Gerald Niemi, University of Minnesota

Ed Rankin, Center for Applied Bioassessment and Biocriteria

Jan Stevenson, Michigan State University

Denice Wardrop, Pennsylvania State University

Chris Yoder, Midwest Biodiversity Institute

Tool #3: The Stressor Identification and Causal Analysis/Diagnosis Decision Information System

(2000 – 2010)

States

Connecticut, Iowa, Maine, Minnesota, Mississippi, Ohio, Washington, West Virginia 

Office of Research and Development: Core Technical Development Team

Laurie Alexander, Susan Cormier, David Farrar, Michael Griffith, Maureen Johnson, Michael McManus, 

Susan Norton, John Paul, Amina Pollard, Kate Schofield, Patricia Shaw-Allen, Glenn Suter, Lester Yuan,

C. Richard Ziegler

For a full list of authors and contributors for this tool, please go to: 

http://www.epa.gov/caddis/caddis_authors.html
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 iv

Disclaimer

The discussion in this document is intended solely to provide information on advancements in the field 

of biological assessments and on use of biological assessments to support state water quality 

management programs. The statutory provisions and the U.S. Environmental Protection Agency (EPA) 

regulations described in this document contain legally binding requirements. This document is not a 

regulation itself, nor does it change or substitute for those provisions or regulations. The document does 

not substitute for the Clean Water Act, a National Pollutant Discharge Elimination System permit, or EPA 

or state regulations applicable to permits; nor is this document a permit or regulation itself. Thus, it 

does not impose legally binding requirements on EPA, states, tribes, or the regulatory community. This 

document does not confer legal rights or impose legal obligations on any member of the public.

While EPA has made every effort to ensure the accuracy of the discussion in this document, the 

obligations of the regulated community are determined by statutes, regulations, and other legally 

binding requirements. In the event of a conflict between the discussion in this document and any 

statute or regulation, this document will not be controlling.

The general descriptions provided here might not apply to a situation depending on the circumstances. 

Interested parties are free to raise questions and objections about the substance of this document and 

the appropriateness of the application of the information presented to a situation. EPA and other 

decision makers retain the discretion to adopt approaches on a case-by-case basis that differ from those 

described in this document where appropriate.

Mention of any trade names, products, or services is not and should not be interpreted as conveying 

official EPA approval, endorsement, or recommendation. 

This is a living document and might be revised periodically. EPA could revise this document without 

public notice to reflect changes in EPA policy, guidance, and advancements in field of biological 

assessments. EPA welcomes public input on this document at any time. Send comments to Susan 

Jackson, Office of Science and Technology, Office of Water, U.S. Environmental Protection Agency, 1200 

Pennsylvania Avenue, Mail Code 4304T, Washington, DC 20460.

The reference section and Appendix A of this document were updated February 2012 to include 

publication dates for USEPA technical documents and website that were originally cited as draft.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 v 

Contents

Foreword........................................................................................................................................ viii

Chapter 1. Incorporating Biological Assessments into Water Quality Management.............................. 1

1.1 Why Is Measuring Biological Condition Important? ..................................................................... 1

1.2 Using Biological Assessment Information in State and Tribal Water Quality Management 

Programs....................................................................................................................................... 3

1.3 Water Quality Program Applications and Case Studies................................................................ 4

Water Quality Standards........................................................................................................... 4

Monitoring and Assessment...................................................................................................... 5

Identification of Impaired and Threatened Waters in States’ Integrated Water Quality 

Reports...................................................................................................................................... 6

Development of Total Maximum Daily Loads........................................................................... 6

National Pollutant Discharge Elimination System Permits........................................................ 7

NPS Pollution............................................................................................................................. 8

Compliance Evaluation and Enforcement Support................................................................... 8

Watershed Protection............................................................................................................... 9

Chapter 2. Tools for Improving the Use of Biological Assessments in Water Quality Management......10

2.1 Tool #1: Biological Assessment Program Review........................................................................ 11

The Program Review Process.................................................................................................. 11

Evaluation of Critical Technical Elements of a State’s or Tribe’s Biological Assessment 

Program................................................................................................................................... 13

2.2 Tool #2: The Biological Condition Gradient................................................................................. 15

What Is the BCG?..................................................................................................................... 15

How Is the BCG Constructed? ................................................................................................. 17

Calibrating the Conceptual Model to Local Conditions........................................................... 19

2.3 Tool #3: Stressor Identification (SI) and Causal Analysis/Diagnosis Decision Information 

System (CADDIS)......................................................................................................................... 22

How Can Biological Information Be Used for Stressor Identification?.................................... 22

Stressor ID/CADDIS.................................................................................................................. 22

Chapter 3. Case Studies....................................................................................................................26

3.1 Protecting Water Quality Improvements and High Quality Conditions in Maine ......................... 28

3.2 Arizona’s Development of Biological Criteria.............................................................................. 31

3.3 Protection of Antidegradation Tier II Waters in Maryland ......................................................... 34

3.4 Using Complementary Methods to Describe and Assess Biological Condition of Streams 

in Pennsylvania ........................................................................................................................... 36

3.5 Use of Biological Assessments to Support Use Attainability Analysis in Ohio............................ 39

3.6 Screening Tool to Assess Both the Health of Oregon Streams and Stressor Impacts................. 42

3.7 North Fork Maquoketa River TMDL in Iowa ............................................................................... 45

3.8 Addressing Stormwater Flow in Connecticut’s Eagleville Brook TMDL for Biological 

Impairment................................................................................................................................. 48

3.9 Vermont’s Use of Biological Assessments to List Impaired Waters and to Support NPDES 

Permit Modification and Wastewater Treatment Facility Upgrades......................................... 50

3.10 Restoration of Red Rock Creek by the Grand Portage Band of Lake Superior Chippewa......... 53

3.11 Using Biological Assessment Data to Show Impact of NPS Controls in Michigan..................... 56
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 vi

3.12 Using Biological Assessment as Evidence of Damage and Recovery Following a Pesticide 

Spill in Maryland and the District of Columbia........................................................................... 58

3.13 Support for Dredge and Fill Permitting in Ohio ........................................................................ 60

3.14 Virginia INSTAR Model for Watershed Protection.................................................................... 62

3.15 Examination of Climate Change Trends in Utah ....................................................................... 65

3.16 Applications of Biological Assessment at Multiple Scales in Coral Reef, Estuarine, and 

Coastal Programs........................................................................................................................ 67

3.17 Partnerships in the Protection of Oregon’s Coho Salmon ........................................................ 72

References.......................................................................................................................................75

Glossary...........................................................................................................................................81

Abbreviations and Acronyms............................................................................................................88

Appendix A. Additional Resources....................................................................................................90

Biological Assessment and Biological Criteria: Technical Guidance.................................................. 90

Other Relevant Water Program Guidance ........................................................................................ 92

Figures

Figure 1-1. Numbers of imperiled North American freshwater and diadromous fish taxa.......................... 1

Figure 1-2. Biological assessments provide information on the cumulative effects on aquatic 

communities from multiple stressors.............................................................................................. 2

Figure 1-3. Biological condition of our nation’s streams.............................................................................. 2

Figure 2-1. Key features of the program review process and examples of commensurate upgrades....... 13

Figure 2-2. The BCG..................................................................................................................................... 16

Figure 2-3. Steps in a BCG calibration......................................................................................................... 19

Figure 2-4. Stressor identification process. ................................................................................................ 23

Figure 3-1. Biological data and assessments support integrated decision making. ................................... 26

Figure 3-2. Comparison of calibrated BCG tier assignments (mean value) and IBI scores for 

freestone streams representing range of conditions from minimal to severely stressed. ........... 37

Tables

Table 2-1. Key features of the technical attributes for levels of rigor in state/tribal biological 

assessment programs (streams and rivers). .................................................................................. 12

Table 2-2. Biological and other ecological attributes used to characterize the BCG.................................. 18

Table 2-3. Example of narrative decision rules for distinguishing BCG Level 2 from Level 3 for 

streams, modified from New Jersey BCG expert workshop.......................................................... 20

Table 3-1. Criteria for Maine river and stream classifications and relationship to antidegradation 

policy.............................................................................................................................................. 29

Table 3-2. Arizona numeric biological criteria IBI scores............................................................................ 33

Table 3-3. Summary of Ohio’s beneficial use designations for the protection of aquatic life in 

streams. ......................................................................................................................................... 39

Table 3-4. Qualitative scoring guidelines for the BMIBI and FIBI. .............................................................. 46
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 vii

Table 3-5. Reference criteria for assessing biological integrity. ................................................................. 46

Table 3-6. BMIBI and FIBI results for the NMFR Watershed....................................................................... 46

Table 3-7. Summary of TMDL analysis for Eagleville Brook........................................................................ 49

Table 3-8. Permit limitations for two textile facilities. ............................................................................... 51

Table 3-9. Macroinvertebrate assessments for Dog River—Northfield WWTF.......................................... 52

Table 3-10. Sampling to assess progress toward restoration goals............................................................ 55

Table 3-11. Plant sampling results.............................................................................................................. 55

Table 3-12. Biological benchmarks. ............................................................................................................ 73
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 viii

Foreword

This guide serves as a primer on the role of biological assessments in a variety of water quality 

management program applications, including reporting on the condition of the aquatic biota, 

establishing biological criteria, and assessing the effectiveness of Total Maximum Daily Load

determinations and pollutant source controls. This guide provides a brief discussion of technical tools

and approaches for developing strong biological assessment programs and presents examples of 

successful application of those tools.

The objective of the Clean Water Act (CWA), and water 

quality management programs generally, is “to restore 

and maintain the chemical, physical, and biological 

integrity of the Nation’s waters.” Although we have 

achieved major water quality improvements over the 

past four decades and have reduced the discharge of 

many toxic chemicals into our nation’s waters, many 

environmental challenges remain, such as loss and 

fragmentation of habitat, altered hydrology, invasive 

species, climate change, discharge of new chemicals, 

stormwater, and nitrogen or phosphorus (nutrient) 

pollution. In the face of such challenges, how can we 

best deploy our water quality programs to meet the 

vision of the CWA for protection of aquatic life? 

Measuring the condition of the resident biota in surface waters using biological assessments and 

incorporating that information into management decisions can be an important tool to help federal, 

state, and tribal water quality management programs meet many of the challenges. Biological 

assessments are an evaluation of the condition of a waterbody using surveys of the structure and 

function of a community of resident biota (e.g., fish, benthic macroinvertebrates, periphyton, 

amphibians) (for more information, see Biological Assessment Key Concepts and Terms)

1

. Assessments 

of habitat condition, both instream and riparian, are typically conducted simultaneously. Such

information can reflect the overall ecological integrity of a waterbody and provides a direct measure of 

both present and past effects of stressors on the biological integrity of an aquatic ecosystem. The 

benefit of a biological assessment program is based in its capability to:

 Characterize the biological condition of a waterbody relative to water quality standards (WQS). 

 Integrate the cumulative effects of different stressors from multiple sources, thus providing a 

holistic measure of their aggregate effect. 

 Detect aquatic life impairment from unmeasured stressors and unknown sources of impairment. 

 Provide field data on biotic response variables to support development of empirical stressor 

response models. 

 Inform water quality and natural resource managers, stakeholders, and the public on the 

environmental outcomes of actions taken.

 

1 http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/upload/primer_factsheet.pdf

Biological integrity has been defined to 

mean the capability of supporting and 

maintaining a balanced, integrated, and 

adaptive community of organisms having a 

composition and diversity comparable to 

that of natural habitats of the region (Frey 

1975; modified by Karr and Dudley 1981). 

Biological assessments can be used to 

directly measure the condition of the biota 

residing in a waterbody and provide 

information on biological integrity. 

Resident biota include species that spend 

all or a part of their life cycle in the aquatic 

environment.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 ix

It is EPA’s long-standing policy that biological assessments should be fully integrated in state and tribal 

water quality programs and used together with whole effluent and ambient toxicity testing, and with 

chemical-specific analyses, to assess attainment of designated aquatic life uses in WQS (USEPA 1991b). 

Each of these methods can be used to provide a valid assessment of aquatic life use impairment.

Biological assessments complement chemical-specific, physical, and whole effluent toxicity measures of 

stress and exposure by directly assessing the response of the community in the field (USEPA 1991a). 

Measurable changes in the biotic community—for example, the return of native species, decrease in 

anomalies and lesions in fish and amphibians, and decrease in pollution-tolerant species paired with an 

increase in pollution-sensitive species—can be readily communicated to the public and the regulated 

community. This can result in greater stakeholder understanding of effects from stressors and support 

for management actions. Additionally, as response-stressor relationships are documented, biological 

assessments in concert with stressor data can be used to help predict and track environmental 

outcomes of management actions.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 1 

Chapter 1. Incorporating Biological Assessments into Water Quality 

Management

1.1 Why Is Measuring Biological Condition Important?

With the passage of the Clean Water Act (CWA) in 1972 and subsequent national investment in water 

infrastructure and regulation, much work has been done to restore rivers, lakes, streams, wetlands, and 

estuaries. However, despite our best efforts and many documented successes, we continue to lose 

aquatic resources (Figure 1-1) (H. John Heinz III Center for Science, Economics, and the Environment 

2008; Jelks et al. 2008; USEPA 2006). Pollutants (e.g., pathogens, metals, nitrogen, phosphorus 

pollution) continue to be major causes of water quality degradation. Additionally, the impact of other 

significant stressors, including habitat loss and fragmentation, hydrologic alteration, invasive species, 

and climate change, can be better understood using analytical tools and information that can operate at 

the ecosystem scale, such as biological assessments. 

Source: Jelks et al. 2008

Figure 1-1. Numbers of imperiled North American freshwater and diadromous fish taxa.

Note: The increase in total number of taxa identified as vulnerable, threatened, or endangered might be due in 

part to improvements in our understanding, naming, and assessing aquatic resources, resulting in more complete 

and accurate assessments.

Biological assessments can be used to directly measure the overall biological integrity of an aquatic 

community and the synergistic effects of stressors on the aquatic biota residing in a waterbody where 

there are well-developed biological assessment programs (Figure 1-2) (USEPA 2003). Resident biota 

function as continual monitors of environmental quality, increasing the sensitivity of our assessments by 

providing a continuous measure of exposure to stressors and access to responses from species that 

cannot be reared in the laboratory. This increases the likelihood of detecting the effects of episodic 

events (e.g., spills, dumping, treatment plant malfunctions), toxic nonpoint source (NPS) pollution 

(e.g., agricultural pesticides), cumulative pollution (i.e., multiple impacts over time or continuous lowlevel stress), nontoxic mechanisms of impact (e.g., trophic structure changes due to nutrient 

enrichment), or other impacts that periodic chemical sampling might not detect. Biotic response to

impacts on the physical habitat such as sedimentation from stormwater runoff and physical habitat 

alterations from dredging, filling, and channelization can also be detected using biological assessments. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 2 

Figure 1-2. Biological assessments provide information on the cumulative effects on aquatic communities 

from multiple stressors. Figure courtesy of David Allen, University of Michigan.

States and tribes have used biological assessments to set environmental goals, detect degradation, 

prioritize management actions, and track improvements (USEPA 2002). Multiple examples of applications 

are presented in Chapter 3. Additionally, the U.S. Environmental Protection Agency (EPA) 2 and 

U.S. Geological Survey (USGS) 3 are conducting national and regional assessments of the condition of 

aquatic communities and the presence and distribution of stressors that affect the aquatic biota. The EPA 

National Aquatic Resource Surveys (NARS) program employs a probability-based sampling design while the 

USGS National Water-Quality Assessment (NAWQA) Program utilizes a targeted design. The data provide a 

baseline for assessing biological conditions and key stressors over time and tracking environmental 

improvements at the national or regional level (Figure 1-3). 

Source: USEPA 2006. 

Figure 1-3. Biological condition of our nation’s streams. In its first survey of stream condition, EPA found that 

28 percent of the nation’s stream miles are in good condition compared to the best existing reference sites in their 

regions, 25 percent are in fair condition, and 42 percent are in poor condition.

 

2 http://water.epa.gov/type/watersheds/monitoring/nationalsurveys.cfm. 

3 http://water.usgs.gov/nawqa. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 3 

1.2 Using Biological Assessment Information in State and Tribal Water Quality 

Management Programs

Biological assessment information has been used by states and tribes to:

 Define goals for a waterbody—Information on the composition of a naturally occurring aquatic 

community can provide a description of the expected biological condition for other similar 

waterbodies and a benchmark against which to measure the biological integrity of surface 

waters. Many states and tribes have used such information to more precisely define their 

designated aquatic life uses, develop biological criteria, and measure the effectiveness of 

controls and management actions to achieve those uses. 

 Report status and trends—Depending on level of effort and detail, biological assessments can 

provide information on the status of the condition of the expected aquatic biota in a waterbody 

and, over time with continued monitoring, provide information on long-term trends. 

 Identify high-quality waters and watersheds—Biological assessments can be used to identify 

high-quality waters and watersheds and support implementation of state and tribal 

antidegradation policies. 

 Document biological response to stressors—Biological assessments can provide information to 

help develop biological response signatures (e.g., a measurable, repeatable response of specific 

species to a stressor or category of stressors). Examples include sensitivity of mayfly species 

(pollution-sensitive aquatic insects) to metal toxicity or temperature-specific preferences of fish 

species. Such information can provide an additional line of evidence to support stressor 

identification and causal analysis (USEPA 2000a), as well as to inform numeric criteria 

development (USEPA 2010a).

 Complement pollutant-specific ambient water quality criteria—Biological assessment

information can complement water quality standards (WQS) by providing field information on 

the cumulative effects on aquatic life from multiple pollutants, as well as detecting impacts from 

pollutants that do not have EPA recommended numeric criteria.

 Complement direct measures of whole effluent toxicity (WET) tests—Biological assessments 

can provide information to help document improvements in aquatic life following actions taken 

to address the aggregate toxic effects of wastewater discharge effluents detected through 

laboratory WET tests. Additionally, biological assessments complement WET tests by directly 

measuring the cumulative or post-impact effects that both point source and NPS contaminants 

have on aquatic biota in the field. 

 Address water quality impacts of climate change—EPA, states, and tribes are exploring how 

biological assessments can be used in concert with physical, chemical, and land use data to help 

identify baseline biological conditions against which the effects of global climate change on 

aquatic life can be studied and compared. Such information could enable a water quality 

management program to calibrate biological assessment endpoints and criteria to adjust for 

long-term climate change conditions. Additionally, long-term data sets will enable trends 

analysis and support predictive modeling and forecast analysis.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 4 

1.3 Water Quality Program Applications and Case Studies

The CWA employs a variety of regulatory and nonregulatory approaches to reduce direct pollutant 

discharges into waterways, finance municipal wastewater treatment facilities, and manage polluted 

runoff. Those approaches are employed to achieve the broader goal of restoring and maintaining the 

chemical, physical, and biological integrity of the nation’s waters. The role of biological assessment 

information to support such approaches is described below, and case studies of successful 

implementation are provided in Chapter 3.

Water Quality Standards

State and tribal WQS programs can use biological assessment information in developing descriptions of

CWA-designated aquatic life uses in terms of the expected biological community. For example, in states 

and tribes that identify high-quality waters for antidegradation purposes on a waterbody-by-waterbody 

basis, biological assessments can provide information to help define and protect existing aquatic life 

uses and identify Tier 2 waters (e.g., where the quality of the waters exceed levels necessary to support 

propagation of fish, shellfish, and wildlife and recreation in and on the water) and Outstanding National 

Resource Waters (ONRWs). Maryland is using biological assessments to help identify high-quality 

streams for antidegradation purposes on a waterbody-by-waterbody basis (case study 3.3).

Pennsylvania is exploring the use of biological assessment information to help assess attainment of 

aquatic life uses and to describe biological characteristics of waters along a gradient of condition (case 

study 3.4). This information may potentially be used to support protection of waters of the highest 

quality that require special protection. Arizona used biological assessments to develop numeric 

biological criteria using the reference condition approach (Stoddard et al. 2006) that takes into account 

the quality of the reference sites (case example 3.2). 

Some states have calibrated biological response to gradients of anthropogenic stress impacting surface 

waters (see Chapter 2, Tool #2, The Biological Condition Gradient). This approach, when applied to WQS

by defining the designated aquatic life uses along a gradient of condition, has provided these states with

the capability to improve waters incrementally, protect high-quality waters, and help identify factors 

that affect attainability. For example, Maine assigns a waterbody to a specific condition class on the 

basis of its current condition and potential for improvement. Numeric biological criteria have been 

developed for each class and adopted into their WQS (case study 3.1). Over the past 30 years, the use 

designations for many streams and rivers in Maine have been upgraded according to documented 

biological improvements and attainment of the biological criteria that define higher quality use classes.

This approach is sometimes referred to as tiered aquatic life uses and has also been implemented by the 

State of Ohio (case study 3.5). 

Additionally, biological assessments can provide information on the species composition at a site under 

consideration for site-specific criteria. Using the species recalculation procedure, a state or tribe can

adjust chemical water quality to reflect the chemical sensitivity of species that occur at a site (USEPA 

1994). Biological assessment information may support modification of the default species sensitivity 

distribution to better reflect the expected community composition at the site. For example, if the site is 

a naturally occurring warm body of water, coldwater fish species could be replaced by resident 

warmwater fish species in the species sensitivity distribution from which a site-specific criterion is 

calculated.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 5 

Monitoring and Assessment 

Biological monitoring and assessments provide data to aquatic resources managers at the local, state, 

tribal, regional, and national levels to help assess status and trends of aquatic resources as well as to

measure the effectiveness of management actions to protect or restore waters. For example, the 

biological monitoring program in Montgomery County, Maryland, produces biological assessment

information on the condition of the County’s streams and the effectiveness of innovative best 

management practices (BMPs) for stormwater control.4 At the state level, the Maryland Department of 

the Environment (MDE) conducts biological monitoring to evaluate permit effectiveness, conduct impact 

assessments, and identify high-quality waters (case studies 3.3 and 3.12). Also, Maryland Department of 

Natural Resources (MDNR)5 provides MDE and the public with a statewide biological assessment of 

status and trends for streams and rivers that may serve as a yardstick for measuring the overall 

effectiveness of local and state management actions.

Biological assessment information has been used by counties and state/tribal agencies to facilitate 

collaboration and effective use of limited resources. For example, two state agencies in Oregon jointly 

conducted biological assessments to address their information needs (case study 3.17). For the Oregon 

Department of Fish and Wildlife (ODFW), monitoring of aquatic benthic macroinvertebrate communities 

in streams and rivers, in conjunction with chemical and physical monitoring, provided important 

information on water quality and habitat conditions identified as critical to coho salmon viability. 

Oregon’s Department of Environmental Quality (ODEQ) used the same biological assessment

information to assess attainment of the designated uses to protect and maintain salmonid populations.

At the national level, biological data from the National Aquatic Resource Surveys6 are being used in 

EPA’s strategic plan to track improvements in water quality for streams, rivers, wetlands, and coastal 

waters. The results of the first national surveys for streams and coastal waters are included in EPA’s 

Report on the Environment.7 These surveys, which incorporate a statistical probabilistic design, are key 

tools for communicating to the public what the Agency knows about the condition of the nation’s 

waters at national and regional scales. The biological components of the national surveys will continue 

to provide nationally consistent indicators of water quality that can be used to gauge the overall effect 

of the national investment in protecting and restoring the nation’s watersheds.

EPA also uses biological assessments to assess status and trends at a regional or large ecosystem scale 

(e.g., in the Upper Mississippi River Basin or the Great Lakes) and measure biological response to 

restoration efforts related to disasters (e.g., Hurricane Katrina and the Gulf of Mexico oil spill). National 

and regional biological assessments provide information that helps facilitate interagency collaboration 

for large-scale restoration and protection efforts. For example, a recent USGS multiregional assessment 

found that alteration of streamflow is a major predictor of biological integrity of both fish and 

macroinvertebrate communities (Carlisle et al. 2010). Alterations in stream flow are associated with 

riparian disturbance and can influence the release of nitrogen, phosphorus, and sediments into streams 

(Poff and Zimmerman 2010). The combined results of national, regional, and state/tribal ecological 

assessments will provide the data needed to predict and better manage future impacts of stressors from 

 

4 For an additional example, see 

http://water.epa.gov/scitech/swguidance/waterquality/standards/criteria/aqlife/biocriteria/npdesmaryland.cfm. 

5 http://www.dnr.state.md.us. 

6 http://water.epa.gov/type/watersheds/monitoring/nationalsurveys.cfm. 

7 http://www.epa.gov/roe. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 6 

human activities such as urban development, water allocation, and agriculture. The results of different 

program actions to address different stressors and their sources can be related to a common measure of 

environmental improvement—the condition of the aquatic biota. 

Identification of Impaired and Threatened Waters in States’ Integrated Water Quality 

Reports 

Under section 303(d) of the CWA and supporting regulations (40 CFR 130.7), states, territories, and 

authorized tribes (hereafter referred to as states) are required to develop lists of impaired and 

threatened waters that require Total Maximum Daily Loads (TMDLs). Impaired waters are those that do 

not meet any applicable WQS, including designated uses, narrative criteria and numeric criteria such as 

biological criteria adopted as a standard. EPA recommends that states consider as threatened those 

waters that are currently attaining WQS, but which are expected to not meet WQS by the next listing 

cycle (every 2 years). Consistent with EPA recommendation, many states consolidate their section 

303(d) and section 305(b) reporting requirement into one “integrated” report.

If biological assessments indicate that a waterbody is impaired or threatened, the waterbody is included 

on the state’s section 303(d) list and scheduled for TMDL development. Some 30 states have used 

biological assessment information as the basis for concluding that designated aquatic life use(s) were 

not supported and included these waters on their section 303(d) lists. In some cases, these listings were 

based on comparison of the biological assessments to state-adopted numeric biological water quality 

criteria. However, in most cases, biological assessments were treated as translations of one or more of a 

state’s narrative water quality criteria or as direct evidence that designated aquatic life uses were not 

supported.

How to reconcile conflicting results among different datasets (e.g., chemical, physical, biological) is 

discussed in EPA’s Integrated Reporting Guidance (IRG) for the 2006 sections 303(d) and 305(b) 

reporting cycle. Also discussed in the IRG, if a designated use, such as aquatic life, is not supported and 

the water is impaired or threatened, the fact that the specific pollutant may not be known does not 

provide a basis for excluding the water from the section 303(d) list.

8 These waters are often identified 

on a state’s list as cause or pollutant unknown. These waters must be included on the list until the 

pollutant is identified and a TMDL completed or the state can demonstrate that no pollutant(s) cause or 

contribute to the impairment. For example, in 1998, Iowa listed a 20-mile segment of the North Fork 

Maquoketa River as aquatic life use impaired—cause unknown, based on biological assessments. Using 

EPA’s CADDIS stressor identification (SI) methodology, Iowa determined that the aquatic life use was 

impaired due to sediments, nutrients, and ammonia (see Tool #3, Stressor Identification and Causal 

Analysis/Diagnosis Decision Information System). A TMDL was developed for each of these pollutants 

and these were approved by EPA in 2007 (case study 3.7).

Development of Total Maximum Daily Loads

Under the CWA, states are required to develop TMDLs for impaired and threatened waters on their 

303(d) lists. States and tribes may use biological assessments to support developing one or more water 

quality targets for the pollutant of concern on the basis of well-documented stressor-response 

relationships, from reference conditions or through use of mechanistic modeling. This is done in 

conjunction with other water quality monitoring data, such as data on concentrations of specific 

 

8 EPA Integrated Reporting Guidance for the 2006 Section 303(d) and 305(b) Reporting Cycle website: 

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/2006IRG_index.cfm
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 7 

stressors and toxicity effects. For example, Connecticut has developed a relationship between pollutant 

loads, stormwater flows, and impervious land cover (IC) for streams in small watersheds with no other 

known point source discharge (case study 3.8). Connecticut used these relationships to develop a TMDL

for a small stream identified as impaired based on biological assessments. Because the cause of 

impairment was unknown, an SI was completed. The SI determined that the most probable cause of 

impairment was the complex array of pollutants transported by stormwater into the stream. The TMDL 

is expressed as a reduction target for specific segments of the stream and is to be implemented through 

reduction of IC where practical and improved stormwater management throughout the watershed. 

Connecticut will evaluate progress toward the TMDL’s implementation using biological assessments in

conjunction with surface water chemistry assessments. 

Additionally, EPA is encouraging states and tribes to develop TMDLs on a watershed basis (e.g., to 

bundle TMDLs together) to enhance program efficiencies and foster more holistic analysis. Ideally, 

TMDLs would be incorporated into comprehensive watershed strategies, while biological assessments 

would provide information on how the aquatic community responds to the full array of restoration 

activities. EPA is launching the Recovery Potential Screening Tools and Resources website (USEPA 

2012),

9 designed to help state, tribal, and other restoration programs evaluate the relative restorability 

of impaired waters and help prioritize TMDL development. The website provides an approach to identify 

the use impaired waters and watersheds most likely to respond well to restoration, as well as 

information on methods, tools, technical information, and instructional examples that managers can 

customize for restoration programs in any geographic locality. Application of a gradient of biological 

response to levels of stress, like the Biological Condition Gradient (BCG) (see Chapter 2, Tool # 2, The 

Biological Condition Gradient), can provide a framework to help assess incremental progress in restoring 

a waterbody’s aquatic life use and report environmental outcomes. 

National Pollutant Discharge Elimination System Permits

Under section 402 of the CWA, point source discharges of pollutants to waters of the United States are 

covered by National Pollutant Discharge Elimination System (NPDES) permits. Under EPA regulations at 

40 CFR 122.44(d), an NPDES permit must contain water quality-based effluents if it is found that a 

discharge will cause, have the reasonable potential to cause, or contribute to an excursion above a 

WQS. States must assess permitted effluent discharges in a manner that is consistent with EPA NPDES 

regulations (40 CFR 122.44).

10 States and tribes can use biological assessment information in addition to 

chemical-specific and WET data to support development of permit conditions that will protect water 

quality, including attainment of state WQS. Data from biological assessments can be used independently 

from, or in combination with, WET or chemical data to assess WQS attainment (USEPA 1991b). If any 

one or a combination of these three assessment methods demonstrates that the applicable WQS are 

not attained, appropriate and corrective action would be taken to address the findings as necessary, 

including compliance with applicable NPDES permit development provisions at 40 CFR PART 

122.44(d)(1).

While narrative biological criteria might exist for many states and some authorized tribes in their WQS, 

in order for biological assessment information to effectively support the NPDES permit process there 

should be an EPA-approved numeric interpretation of the narrative biological criteria. States and tribes 

that have adopted biological criteria in their WQS may benefit from the use of biological assessment 

 

9 EPA Recovery Potential Screening website: http://www.epa.gov/recoverypotential. 

10 For more information on NDPES regulations, go to http://cfpub.epa.gov/npdes/regs.cfm?program_id=45. 
A Primer on Using Biological Assessments to Support Water Quality Management

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data as an additional biological check of permit controls, including limits, to see if they result in abating 

pollutant impacts, restoring water quality, or preventing further degradation. In addition, biological 

assessments as a “special studies/additional monitoring” permit condition can be used to assess overall 

permit effectiveness to control source pollutant(s) and used as an NPDES permit trigger to reopen and 

potentially modify the permit11 if the biological assessment studies indicate that the permitted discharge 

continues to impact the receiving waterbody.

Also, while biological assessments can establish that aquatic life use impairment exists in the area of the 

discharge, the cause of the impairment might be wholly or partially due to point sources or NPS 

pollution. In such cases, an NPDES permit could establish controls based on the portion of impairment 

that is related to the effluent. Thus, additional chemical analysis and WET tests and/or source 

identification are typically conducted. For example, Vermont has used biological assessment information 

to support changes to effluent limits for metals on the basis of impact analysis, WET tests, and 

documented stressor-response relationships between metals and the aquatic biota (case study 3.9). 

That information helped support requiring additional treatment technologies that resulted in improved 

water quality. Upstream and downstream biological assessments were part of the follow-up monitoring 

plan and, with chemical and WET data, documented the resulting improvements in ambient biological 

and chemical conditions. Thus, in conjunction with required NPDES effluent monitoring such as WET and 

chemical-specific information, Vermont used biological assessments and its EPA-approved biological 

criteria to support narrative NPDES permit requirements to protect aquatic life. Currently Vermont has 

refined aquatic life uses (e.g., tiered aquatic life uses) and narrative biological criteria in its WQS 

supported by published peer-reviewed technical procedures for translating the narrative biological 

criteria into a numeric threshold.

NPS Pollution

Biological assessments can be a sensitive indicator of cumulative effects from multiple and unpredictable 

stressors from NPS pollution. Tracking water quality conditions using biological assessments is one way to 

assess whether the biological community is affected by NPS pollution and that efforts to improve degraded 

waters using voluntary BMPs are effective. In managing NPS pollution, a natural resource agency could 

initiate cooperative land use programs in an area or install BMPs to improve the water resource and 

establish biological goals as a benchmark for restoration. Before-and-after biological assessments 

compared to the biological benchmark make it possible to evaluate the success of management actions. 

For example, Michigan has used biological assessments to help determine biological impairments, target 

restoration efforts, and monitor results in Carrier Creek (case study 3.11).

Compliance Evaluation and Enforcement Support 

Regulatory authorities can use biological assessment information to support enforcement actions by 

helping to document biological impacts and measure recovery of the aquatic community due to 

mitigation and cleanup actions. For example, a fish kill in a tributary to the Potomac River in Maryland 

and the District of Columbia was caused by illegal dumping of pesticide wastes in Maryland. Biological 

and chemical sampling data were used to locate the source of the pesticide wastes, identify the 

responsible party, and show subsequent improvements in water quality as a result of enforcement 

activities (case study 3.12). Biological assessment information, in conjunction with biological assays and 

chemical and physical assessments, can assist enforcement agencies in assessing damage and levying 

 

11 As prescribed under NPDES regulatory requirements for permit reopeners/modifications (CFR 122.44). For more 

information on NDPES regulations, go to http://cfpub.epa.gov/npdes/regs.cfm?program_id=45. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 9 

fair and reasonable damage assessments on those proven responsible for toxic spills, and determining 

the rate and level of stream recovery.

Watershed Protection

Increasingly, EPA, states, territories, and tribes are implementing CWA programs on an integrated 

watershed basis—including air, land, and ecosystem relationships and related regulatory tools such as 

those used in the Chesapeake Bay12 and the National Estuary programs (NEPs)13 (USEPA 2007). 

Biological assessments are used in watershed-level programs to help define ecological goals and assess 

progress in achieving those goals. Recently, EPA has embarked on the Healthy Watershed Initiative, 

which focuses on protecting high-quality waters and watersheds (USEPA In draft). It is a strategic 

approach that identifies healthy waters and watersheds at the state level and then targets resources at 

both the state and local levels for their protection. Biological assessments provide critical information 

and measurable benchmarks to identify high-quality waters in healthy watersheds and then, over time, 

evaluate how effectively such systems are being protected. The State of Virginia is using biological 

assessments in its own Healthy Watersheds initiative to define protection and restoration goals that 

resonate with the public (case study 3.14). EPA’s Office of Research and Development (ORD) is working 

with several states, territories, and NEPs to develop biological assessment tools and approaches that can 

be applied at multiple scales to protect estuarine and coastal ecosystems and their watersheds (case 

study 3.16). Additionally, the BCG (see Chapter 2, Tool # 2) can be applied as a field-based assessment 

framework to describe the health of waterbodies and their watersheds and communicate the biological 

condition to the public (USEPA In draft). And, in conjunction with refined aquatic life uses and biological 

criteria adopted into WQS, a BCG-like framework can be used to support management actions to 

protect existing high-quality waters in a healthy watershed, as demonstrated by the State of Maine

(case study 3.1). 

 

12 Chesapeake Bay Program website: http://www.chesapeakebay.net. 

13 National Estuary Program website: http://water.epa.gov/type/oceb/nep/estuaries_index.cfm. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 10

Chapter 2. Tools for Improving the Use of Biological Assessments in 

Water Quality Management

EPA has published several documents that provide guidance on incorporating biological assessment 

information into water quality programs, many of which have been in use for several years. They include 

technical guidance on developing biological criteria and general program guidance on application of 

biological assessment information in different water quality programs. A summary of these documents 

is provided in Appendix A. Additionally, other technical support documents, or technical tools, have 

been recently developed to further assist states and tribes in developing robust biological assessment 

programs and applying biological assessment information. Three of these recent tools are listed below 

and briefly summarized in the following pages. 

 Tool #1: The Biological Assessment Program Review. The level of program rigor determines 

how well the monitoring and assessment program produces the information needed to support 

management decision making. A review process and checklist have been developed and piloted 

by regions, states, and tribes to help assess the technical capability of a state or tribal biological 

assessment program and strategically determine where to invest resources to develop a 

technically robust biological assessment program.

 Tool #2: The Biological Condition Gradient (BCG). The BCG is a conceptual model that describes 

how biological attributes of aquatic ecosystems might change along a gradient of increasing 

anthropogenic stress. The model can serve as a template for organizing field data (biological, 

chemical, physical, landscape) at an ecoregional, basin, watershed, or stream segment level. A 

BCG calibrated with field data can help states and tribes more precisely define biological 

expectations for their designated aquatic life uses, interpret current condition relative to CWA 

objective and goals, track biological community response to management actions, and 

communicate environmental outcomes to the public. The BCG was designed to help map 

different biological indicators on a common scale of biological condition to facilitate 

communication among programs and across jurisdictional boundaries. The BCG is currently

being field tested in several regions and states.

 Tool #3: Stressor Identification (SI) and Causal Analysis/Diagnosis Decision Information System 

(CADDIS). In 2010 EPA updated its technical support document on causal analysis and literature 

database to help states and tribes identify the most probable cause of impairment to a 

waterbody. Specific databases on biological response to stress have been compiled and will 

undergo continuous updating so that the best available and peer-reviewed literature will be 

accessible as part of CADDIS. This document and database will assist states that have listed 

waters as impaired on the basis of biological assessments when the cause of impairment is not 

known.
A Primer on Using Biological Assessments to Support Water Quality Management

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2.1 Tool #1: Biological Assessment Program Review

The information provided below describes technical elements of a biological assessment program, 

summarizes the process and benefits of conducting a program review, and discusses regional/state pilot

programs. 

The Program Review Process

The critical technical elements review is a systematic process to evaluate biological assessment program 

rigor and to identify logical next steps for overall program improvement. The document provides a template

for evaluating critical technical components of a biological assessment program that are scored to arrive at 

a level of program rigor, from level 1 (the least rigorous) to level 4 (the most rigorous) (Table 2-1). The 

review provides a framework for identifying programmatic strengths and weaknesses and helps program 

managers and technical staff members determine key tasks to upgrade the technical abilities of their 

program (Figure 2-1). The evaluation process also identifies opportunities to improve integration of WQS 

and monitoring and assessment programs. This review process was initially piloted in EPA Region 5 and 

more recently applied and further refined in Region 1. Initial programs reviews have focused on biological 

assessments of streams and rivers, but with some refinements in methodology this evaluation process can 

be applied to other types of waterbodies. The states have used the results of the review to target resources 

and prioritize actions to strengthen the technical basis of their biological assessment programs. 

The first part of the review involves discussion on the design of the existing monitoring and assessment

program, the degree to which there is systematic collection of data from the environment, and how well the 

data analysis produces information suitable for making the various decisions asked of it—such as

determining attainment of aquatic life uses, identifying high-quality waters for antidegradation purposes on a 

waterbody-by-waterbody basis, evaluating the severity and extent of impairments, and supporting causal

analysis and pollutant source identification (i.e., toxicity identification evaluation [TIE] and toxicity reduction 

evaluation [TRE]). It is essential that experts in the different program areas be engaged in the discussions to 

help ensure that data quality and information requirements are accurately represented and properly

implemented, especially with regard to EPA-published methodologies. The information helps document how 

monitoring and assessment information is used to support the reporting requirements mandated by the 

CWA and other state or tribal efforts to characterize the status of waterbodies and plan for implementing

restoration efforts. This part of the program review might also examine how the state or tribe uses biological 

assessment information to more precisely define aquatic life uses and develop biological criteria. 

Purpose: To provide a stepwise process to assist states in evaluating the technical capability 

of their biological assessment programs and to strategically determine where to invest 

resources to enhance the technical capability of their programs. 

This tool can be used to answer questions, including the following: 

• Does the quality of data being generated support the management decisions I need 

to make?

• What are the strengths and needs of my existing program?

• How do I build on my current program and further strengthen it?

Source: EPA’s website on key concepts for using biological indicators:

http://www.epa.gov/bioiweb1/html/keyconcepts.html
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Table 2-1. Key features of the technical attributes for levels of rigor in state/tribal biological assessment programs (streams and rivers). 

(Terms in the table are included in the glossary, this template can be modified and applied to other waterbody types.) 

Key features

Attributes of levels of biological assessment program rigor

Level 1 Level 2 Level 3 Level 4

Temporal 

and spatial 

coverage

Variable data collection 

times; upstream/downstream 

and fixed stations

Index period for convenience; nonrandom design at a coarse scale 

(e.g., 4- to 8-digit hydrologic unit 

code [HUC])

Calibrated seasonal index 

periods; statewide spatial design 

using rotating basins at a coarse 

scale (e.g., 4- to 8-digit HUC)

Scientifically-derived temporal 

sampling for management decisions;

multiple spatial designs for multiple 

issues; 11- to 14-digit HUC

Natural 

classification

of aquatic 

ecosystems

No partitioning of natural 

variability; no incorporation 

of differences in stream 

characteristics such as size, 

gradient

Classification usually a geo-graphical 

or other similar organization (e.g.,

fishery-based cold or warmwater;

lacks intra-regional strata [size, 

gradient])

Classification based on a

combination of landscape 

features and physical habitat 

structure; considers all intraregional strata and specific 

ecosystems

Fully partitioned and stratified 

classification scheme that transcends 

jurisdictions and recognizes 

zoogeographical aspects of 

assemblages

Reference 

conditions

No reference conditions; 

presence and absence of key 

taxa are based on best 

professional judgment 

A site-specific control or paired 

watershed approach can be used for 

assessment; regional reference sites 

are lacking

Reference conditions used in 

watershed assessments; regional 

reference sites are too few in 

number or spatial density

Regional reference conditions are 

established in the applicable 

waterbody ecotypes and aquatic 

resource classes

Sampling 

and sample 

processing 

Approach is cursory and relies 

on operator skill and best 

professional judgment, 

producing highly variable and 

less comparable results

Textbook methods are used rather 

than in-house development of 

standard operating procedures to 

specify methods

Methods are calibrated for state

purposes and are detailed and 

well documented; supported by 

in-house testing and

development

Same as Level 3, but methods cover 

multiple assemblages; high 

taxonomic resolution

Data 

management

Sampling event data are 

organized in a series of 

spreadsheets 

Separate databases are used for 

physical, chemical, and biological 

data with separate GIS shapefiles of 

sites

A true relational database is 

specifically designed to include 

data validation checks (e.g., 

Oracle, SQL Server, Access)

Relational database of biological 

assessment data with automated 

data review validation tools and 

geospatial analysis

Biological 

endpoints 

and 

thresholds

Assessment based on 

presence or absence of 

targeted or key species; 

attainment thresholds are not 

specified and no BCG

A biological index or endpoint is by 

specific waterbodies; single 

dimension measures used

A biological index, or model, 

developed and calibrated for use 

throughout the state for the 

various waterbody types

Biological indexes, or models, for 

multiple assemblages are developed 

and calibrated for a state and uses 

the BCG

Causal

analysis

Support for causal analysis is 

lacking

Coarse indications of response via 

assemblage attributes at gross level 

(i.e., general indicator groups)

Developed indicator guilds and 

other aggregations to support 

causal associations; diagnostic 

capability is supported by studies

Response patterns are most fully 

developed and supported by 

extensive research and case studies 

across spatial and temporal scales
A Primer on Using Biological Assessments to Support Water Quality Management

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Figure 2-1. Key features of the program review process and examples of commensurate upgrades.

Evaluation of Critical Technical Elements of a State’s or Tribe’s Biological Assessment 

Program 

The program review evaluates 13 critical technical elements of a biological assessment program 

associated with design, methods, and data interpretation (e.g., survey design, method of classification, 

procedures to establish reference conditions, protocols for sampling collection and processing, data

management and analysis, formal peer review). On the basis of the discussions in the first phase of the 

review, where program information needs are identified, a list of recommendations is developed 

according to the strengths and gaps identified in the technical program evaluation. The 

recommendations are presented in a logical, stepwise progression so that a state or tribe can build on 

its technical program strengths and target resources effectively to address the program gaps.

Participation of program managers and technical staff representing different water quality programs is 

important in the review to build a shared understanding and broad perspective on existing use of 

biological assessment information and begin to identify the technical program gaps and areas for 

improved use.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 14

Case Example: Technical Evaluations in Minnesota and Connecticut

The Minnesota Pollution Control Agency (MPCA) decided in 2005 to use biological assessment

information to develop refined aquatic life uses and numeric biological criteria in its WQS to meet 

its objectives of setting management goals for waterbodies on the basis of their best potential 

condition. MPCA also found biological assessment information as useful to educate and engage 

stakeholders and the public. MPCA used the Critical Technical Elements Program Evaluation 

process to determine where its program was in 2005 and what tasks were yet to be accomplished 

to reach its stated goals. Using the findings, MPCA developed a detailed plan for developing a 

technical program sufficiently rigorous to support adoption in the state’s WQS in 2011–2014 of 

the most appropriate aquatic life uses and numeric biological criteria. MPCA continues to follow 

the plan, addressing the priority recommendations identified in the program evaluation, and is 

proceeding with biological criteria development. As part of this effort, MPCA is exploring 

application of the BCG, the second tool discussed in this document, to develop biological goals for 

their waters that are tailored to specific waterbody types and uses.

The Connecticut Department of Environmental Protection (CT DEP) has been monitoring aquatic 

biological conditions using benthic macroinvertebrates since the late 1980s and has steadily 

upgraded its technical program over the years. The state operates a statewide monitoring and 

assessment program that includes multiple spatial designs to produce both statewide 

assessments using probabilistic design and listings of impaired waters using targeted sampling 

design. CT DEP underwent a Critical Elements Program Evaluation in 2006 to help identify and 

prioritize additional technical program improvements needed to develop numeric biological 

criteria for different levels of quality along a gradient of condition (e.g., excellent and good quality 

waters). The program was evaluated at a level 2 with specific tasks identified to build its technical 

capability (e.g., improved spatial resolution in watershed assessment design from 8-digit HUC to 

10- to 12-digit HUC; a regionally-calibrated multimetric index for benthic macroinvertebrates and 

one for fish that distinguishes between coldwater and warmwater assemblages; instituting an 

independent peer review process). Since the review, CT DEP has improved the technical capability 

of the biological assessment program to a level 3 and now has two numeric indices and enhanced 

spatial monitoring design.

These examples show how states and tribes can use the results of the Critical Elements Program 

Evaluation to develop a blueprint for making orderly improvements and attaining the technical 

proficiency to respond to management questions and improve decision making—including 

support for condition assessments, attainment of WQS, diagnosis of biological impairment, and 

effectiveness monitoring. The program review process identifies specific and successive 

improvements that are needed to improve the rigor of the biological assessment program and a 

checklist so that progress can be identified and tracked.
A Primer on Using Biological Assessments to Support Water Quality Management

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2.2 Tool #2: The Biological Condition Gradient

This section provides an overview of the BCG and how it can be calibrated for specific use by a state or 

tribe. The BCG is being applied and tested in several regions and states.

What Is the BCG?

Over the past 40 years, states have independently developed technical approaches to assess biological 

condition and set designated aquatic life uses for their waters. The BCG was designed to provide a means

to map different indicators on a common scale of biological condition to facilitate comparisons between 

programs and across jurisdictional boundaries in context of the CWA. The BCG is a conceptual, narrative 

model that describes how biological attributes of aquatic ecosystems change along a gradient of increasing 

anthropogenic stress. It provides a framework for understanding current conditions relative to natural, 

undisturbed conditions (Figure 2-2). Some states, such as Maine and Ohio, have used a framework similar 

to the BCG to more precisely define their designated aquatic life uses (case studies 3.1 and 3.5).

Agreeing that, even in different geographic and climatological areas, a similar sequence of biological 

alterations occurs in streams and rivers in response to increasing stress, biologists from across the 

United States developed the model (Davies and Jackson 2006). The model shows an ecologically based 

relationship between the stressors affecting a waterbody (e.g., physical, chemical, biological impacts) and 

the response of the aquatic community (i.e., biological condition). The model is consistent with ecological 

theory and can be adapted or calibrated to reflect specific geographic regions and waterbody type 

(e.g., streams, rivers, wetlands, estuaries, lakes). Approaches to calibrate the BCG to region-, state-, or 

tribe-specific conditions are being piloted in several ecological regions by multiple states and tribes.

In practice, the BCG is used to first identify the critical attributes of an aquatic community (see Table 2-2) 

and then describe how each attribute changes in response to stress. Practitioners can use the BCG to 

interpret biological condition along a standardized gradient, regardless of assessment method, and 

apply that information to different state or tribal programs. For example, Pennsylvania is exploring the 

use of a BCG calibrated to its streams to complement its existing biological indices for 

macroinvertebrates and to describe the biological characteristics of waters along a gradient of 

condition. The state is evaluating using this information to help assess aquatic life use impairments and 

to describe waters of the highest quality (case study 3.4).

Purpose: To provide a common scale of biological condition to support comparisons 

between programs and across jurisdictional boundaries.

This tool can be used to help answer questions, including the following: 

• What biological community should be at a site, e.g., natural conditions?

• Are we protecting our high-quality waters?

• Are we making progress to restore our degraded systems?

• Are our actions making real and lasting environmental improvements?

Source: The biological condition gradient: A descriptive model for interpreting change in 

aquatic ecosystems (Davies and Jackson 2006)
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Source: Modified from Davies and Jackson 2006. 

Figure 2-2. The BCG.

Note: The BCG was developed to serve as a scientific framework to synthesize expert knowledge with empirical 

observations and develop testable hypotheses on the response of aquatic biota to increasing levels of stress. It is 

intended to help support more consistent interpretations of the response of aquatic biota to stressors and to 

clearly communicate this information to the public, and it is being evaluated and piloted in several regions and 

states.

The BCG model provides a framework to help water quality managers do the following: 

 Decide what environmental conditions are desired (goal-setting)—The BCG can provide a 

framework for organizing data and information and for setting achievable goals for waterbodies

relative to “natural” conditions (e.g., condition comparable or close to undisturbed or minimally 

disturbed condition). 

 Interpret the environmental conditions that exist (monitoring and assessment)—Practitioners 

can get a more accurate picture of current waterbody conditions. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 17

 Plan for how to achieve the desired conditions and measure effectiveness of restoration—The 

BCG framework offers water program managers a way to help evaluate the effects of stressors 

on a waterbody, select management measures by which to alleviate those stresses, and 

measure the effectiveness of management actions.

 Communicate with stakeholders—When biological and stress information is presented in this 

framework, it is easier for the public to understand the status of the aquatic resources relative 

to what high-quality places exist and what might have been lost.

How Is the BCG Constructed?

The BCG is divided into six levels of biological conditions along the stressor-response curve, ranging from 

observable biological conditions found at no or low levels of stress (level 1) to those found at high levels 

of stress (level 6) (Figure 2-2). The technical document provides a detailed description of how 10 

attributes of aquatic ecosystems change in response to increasing levels of stressors along the gradient, 

from level 1 to 6 (see Table 2-2). The attributes include several aspects of community structure, 

organism condition, ecosystem function, spatial and temporal attributes of stream size, and 

connectivity. 

Each attribute provides some information about the biological condition of a waterbody. Combined into 

a model like the BCG, the attributes can offer a more complete picture about current waterbody 

conditions and also provide a basis for comparison with naturally expected waterbody conditions. All 

states and tribes that have applied a BCG used the first seven attributes that describe the composition 

and structure of biotic community on the basis of the tolerance of species to stressors and, where 

available, included information on the presence or absence of native and nonnative species and, for fish 

and amphibians, observations on overall condition (e.g., size, weight, abnormalities, tumors).

The last three BCG attributes of ecosystem function and connectance and spatial and temporal extent of 

detrimental effects can provide valuable information when evaluating the potential for a waterbody to 

be protected or restored. For example, a manager can choose to target resources and restoration 

activities to a stream where there is limited spatial extent of stressors or there are adjacent intact 

wetlands and stream buffers or intact hydrology versus a stream with comparable biological condition 

but where adjacent wetlands have been recently eliminated, hydrology is being altered, and stressor 

input is predicted to increase. Pennsylvania is evaluating indicators comparable to the BCG spatial and 

connectance attributes IX and X to characterize the biological conditions of streams in healthy 

watersheds where resources may be well spent to successfully protect such waters (see case study 3.4). 

Additionally, several of EPA’s NEPs, in conjunction with EPA ORD, are exploring application of those 

attributes at a whole-estuary scale (e.g., distribution and connectance of critical aquatic habitats and 

associated biota) (see case study 3.16). 

Additionally, individual attributes might uniquely respond to a specific stressor or group of associated 

stressors (biological response signatures) (Yoder and Rankin 1995; Yoder and Deshon 2003). That 

information could contribute to the causal analysis of biological impairment discussed in Tool #3,

Stressor Identification (SI) and Causal Analysis/Diagnosis Decision Information System (CADDIS). 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 18

Table 2-2. Biological and other ecological attributes used to characterize the BCG. 

Attribute Description

I. Historically documented, 

sensitive, long-lived, or 

regionally endemic taxa

Taxa known to have been supported according to historical, museum, or archeological records, or 

taxa with restricted distribution (occurring only in a locale as opposed to a region), often due to 

unique life history requirements (e.g., sturgeon, American eel, pupfish, unionid mussel species). 

II. Highly sensitive (typically 

uncommon) taxa

Taxa that are highly sensitive to pollution or anthropogenic disturbance. Tend to occur in low 

numbers, and many taxa are specialists for habitats and food type. These are the first to disappear 

with disturbance or pollution (e.g., most stoneflies, brook trout [in the east], brook lamprey). 

III. Intermediate sensitive 

and common taxa 

Common taxa that are ubiquitous and abundant in relatively undisturbed conditions but are 

sensitive to anthropogenic disturbance/pollution. They have a broader range of tolerance than 

attribute II taxa and can be found at reduced density and richness in moderately disturbed sites

(e.g., many mayflies, many darter fish species). 

IV. Taxa of intermediate 

tolerance

Ubiquitous and common taxa that can be found under almost any conditions, from undisturbed to 

highly stressed sites. They are broadly tolerant but often decline under extreme conditions (e.g., 

filter-feeding caddisflies, many midges, many minnow species). 

V. Highly tolerant taxa Taxa that typically are uncommon and of low abundance in undisturbed conditions but that 

increase in abundance in disturbed sites. Opportunistic species able to exploit resources in 

disturbed sites. These are the last survivors (e.g., tubificid worms, black bullhead). 

VI. Nonnative or 

intentionally introduced 

species

Any species not native to the ecosystem (e.g., Asiatic clam, zebra mussel, carp, European brown 

trout). Additionally, there are many fish native to one part of North America that have been 

introduced elsewhere.

VII. Organism condition Anomalies of the organisms; indicators of individual health (e.g., deformities, lesions, tumors).

VIII. Ecosystem function Processes performed by ecosystems, including primary and secondary production; respiration; 

nutrient cycling; decomposition; their proportion/dominance; and what components of the 

system carry the dominant functions. For example, shift of lakes and estuaries to phytoplankton 

production and microbial decomposition under disturbance and eutrophication.

IX. Spatial and temporal 

extent of detrimental 

effects

The spatial and temporal extent of cumulative adverse effects of stressors; for example,

groundwater pumping in Kansas resulting in change in fish composition from fluvial dependent to 

sunfish.

X. Ecosystem connectance Access or linkage (in space/time) to materials, locations, and conditions required for maintenance 

of interacting populations of aquatic life; the opposite of fragmentation. For example, levees 

restrict connections between flowing water and floodplain nutrient sinks (disrupt function); dams 

impede fish migration, spawning.

Source: Modified from Davies and Jackson 2006. 
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Calibrating the Conceptual Model to Local Conditions

The BCG can serve as a starting point for defining the response of aquatic biota to increasing levels of 

stress in a specific region. Although the BCG was developed primarily using forested stream ecosystems, 

the model can be applied to any region or waterbody by calibrating it to local conditions using specific 

expertise and local data. To date, most states and tribes are calibrating the BCG using the first seven 

attributes that characterize the biotic 

community primarily on the basis of tolerance 

to stressors, presence/absence of native and 

nonnative species, and organism condition. 

Although the model has been developed for six 

levels of condition, six levels might not be 

necessary or feasible depending on limitations 

in data or level of technical rigor (see Chapter 2, 

Tool #1, Biological Assessment Program 

Evaluation) or naturally occurring conditions. 

For example, ephemeral streams in the arid 

Southwest naturally support a community of 

aquatic organisms that tolerate extreme 

conditions that range from intense, monsoonlike precipitation to extensive periods of 

drought. Those organisms might also be able to 

tolerate the presence of stressors. Thus, the 

range of response to anthropogenic stress in 

such streams (e.g., moderately tolerant to very 

tolerant species) might be abbreviated 

compared to that of a forested stream 

community in a temperate climate (e.g., very 

sensitive to very tolerant species). Three or four 

tiers might be suitable for those waters.

It is a multistep process to calibrate a BCG to local conditions (Figure 2-3). That process is followed to 

describe the native aquatic assemblages under natural conditions; identify the predominant regional 

stressors; and describe the BCG, including the theoretical foundation and observed assemblage 

response to stressors. Calibration begins with the assembly and analysis of biological monitoring data. 

Next, a calibration workshop is held in which experts familiar with local conditions use the data to define 

the ecological attributes and set narrative statements. For example, narrative decision rules for 

assigning sites to a BCG level on the basis of the biological information collected at sites. New Jersey is 

one of several states that are field testing this approach. Documentation of expert opinion in assigning 

sites to tiers is a critical part of the process. A decision model can then be developed that encompasses 

those rules and is tested with independent data sets. A decision model based on the tested decision 

rules is a transparent, formal, and testable method for documenting and validating expert knowledge

(see Table 2-3 for examples). A quantitative data analysis program can then be developed using those 

rules. EPA recommends peer review of model.

Figure 2-3. Steps in a BCG calibration. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 20

Table 2-3. Example of narrative decision rules for distinguishing BCG Level 2 from Level 3 for streams, 

modified from New Jersey BCG expert workshop

Attributes Rules for BCG Level 2

Structure and function of community 

similar to natural community with 

some additional taxa and biomass

Rules for BCG Level 3

Evident changes in structure due to 

loss of some rare native taxa; shifts in 

relative abundance

Total taxa More than 12 taxa More than 12 taxa

Highly Sensitive Taxa 

(Attribute II only)

More than two taxa May be absent 

Richness of Sensitive Taxa 

(combination of Attributes II 

and III,see table 2-2) 

Attribute II + Attribute III are more 

than 50% of total taxa richness

Attribute II + Attribute III are more 

than 35% of total taxa richness

Abundance of Tolerant Taxa 

(Attribute V) 

Abundance of Attribute V is less than 

20% of community

Abundance of Attribute V is less than 

50% of community

In the example above, both BCG levels 2 and 3 support comparable levels of overall taxa (e.g., total 

taxa). However, there is a shift from BCG level 2 to BCG level 3 in proportion and abundance of sensitive 

and tolerant taxa (e.g., a decrease in proportion of sensitive taxa and an increase in abundance of

pollution-tolerant taxa). The BCG describes incremental shifts in community composition and other 

biological parameters along a gradient of increasing anthropogenic stress. The BCG can be used to 

detect measurable changes in the aquatic biota before there is a complete loss of a certain type or 

category of taxa such as loss of pollution sensitive or native species. This tool will enable earlier 

detection and support action to prevent loss of species or other biological changes. This tool can be used 

to raise the discriminatory power of biological assessment programs in a nationally consistent, 

transparent manner. Narrative decision rules are the first step in formalizing expert opinion and 

expressing empirical findings that can then be tested and validated.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 21

Case Example: New Jersey BCG Calibration

New Jersey developed and calibrated a BCG for its upland streams. The New Jersey Department of 

Environmental Protection (NJ DEP) convened an expert panel workshop that included aquatic 

biologists and water quality experts familiar with the aquatic fauna that inhabit these streams. The 

panel developed descriptions of the ecological attributes for these streams in New Jersey and created 

the narrative rules for assigning sites to levels along the stressor gradient.

The expert panel reviewed the list of taxa from the New Jersey Ambient Biological Monitoring

Network to assign taxa to attributes I–VI. Next, the panel examined macroinvertebrate data from 58 

upland stream sites and reached consensus on the level assignments for all sites reviewed. The panel 

was able to distinguish five separate levels (levels 2–6, see below) for New Jersey upland streams. The 

first level described in Davies and Jackson (2006) consists of entirely pristine sites and was not 

included because the panel could not identify any level 1 (pristine) sites in New Jersey.

On the basis of the characterization of sites identified as belonging to different BCG levels, the panel 

developed a set of narrative decision rules and descriptions for distinguishing among the levels.

BCG level 2 (Minimal changes in structure and function)—Because of extensive historical land 

clearing, cultivation, and early industrial use followed by abandonment and reforestation from the 

early 20th century, the least stressed watersheds are thought to reflect at best BCG level 2. Most of 

the 19th century legacy is in changed stream morphology and hydrology that persist in valley 

bottoms (Walter and Merritts 2008). Watersheds are predominantly forested, with recreational use 

but little residential or agricultural use. The group consensus was that several richness criteria (i.e., 

total taxa, highly sensitive taxa, and all sensitive taxa) must all be met for a site to be considered to 

be in level 2.

BCG level 3 (Evident changes in structure and function)—A typical level 3 stream has a largely 

forested watershed but some areas of suburban development or limited agriculture. Criteria for 

level 3 are similar to those for level 2, but richness of the sensitive organisms is somewhat reduced 

and sensitive organisms do not numerically dominate the assemblage. All the criteria for level 3 

were considered critical.

BCG level 4 (Moderate changes in structure and function)—Typical level 4 streams in New Jersey 

often have relatively extensive suburban and commercial development, some agricultural land use, 

but substantial areas of natural land cover, often mixed with residential areas. In BCG level 4, the 

sensitive taxa are present and still constitute a significant fraction of the community, but they are 

far reduced below their dominance in level 2 and their subdominance in level 3. The assemblage 

has degraded but maintains ecosystem functions as represented by the sensitive taxa.

BCG level 5 (Major changes in structure and function)—BCG level 5 is discriminated from level 4 by 

a significant reduction of sensitive taxa (attributes II and III) to the point where they are merely 

incidental if present and are not a functional part of the community. Although BCG level 5 can have 

high abundance and high taxa richness, the assemblage is dominated by intermediate and tolerant 

taxa, and sensitive taxa have all but disappeared.

BCG level 6 (Severe changes in structure and function)—BCG level 6 reflects nearly complete 

disruption and degradation of the biological community to either very low abundance (less than 50 

organisms in New Jersey’s standard sampling procedure) or very low taxon richness. While 

extremely low abundance often indicates toxic conditions, extremely low richness coupled with 

high abundance often indicates organic enrichment and high-density urban runoff.

New Jersey is considering using the calibrated BCG and the narrative decision rules to help identify 

high-quality waters on a waterbody-by-waterbody basis for antidegradation purposes. 
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October 2011 22

2.3 Tool #3: Stressor Identification (SI) and Causal Analysis/Diagnosis Decision 

Information System (CADDIS)

This section describes how biological assessment information can be used to help identify stressors for 

impaired waters where cause of impairment is unknown. 

How Can Biological Information Be Used for Stressor Identification? 

Once a biological impairment has been determined, water quality managers examine existing water 

quality and landscape data and information to determine the cause and source of impairment, also 

known as stressor identification (SI). Typically, states and tribes identify the probable causes of the 

impairment and then, step-by-step, implement additional controls or management practices (or both) to 

fix the problem. Monitoring the response of the biota to management actions then helps to provide the 

necessary information on whether the primary stressors were correctly identified and the management 

actions effective. The biological response information provided in the initial assessment often includes 

useful information for identifying stressors; for example, the relationship between biological indicators 

and stressors such as the disappearance of certain benthic species sensitive to a specific toxin (e.g., 

sensitivity of aquatic life stage of mayflies to metal toxicity) or a shift in dominate community traits 

related to the increase of a stressor (e.g., a change in primary producer base because of zebra mussel 

invasion). Additionally, states and tribes have successfully implemented management actions that 

address co-occurring stressors supported by documented improvements in water quality. Maryland and 

the District of Columbia were able to use biological assessment data to document the biological effects 

of a pesticide spill that resulted in a fish kill in Rock Creek, a tributary to the Potomac River. The 

information was used as the basis for enforcement actions, and subsequent data were able to support a 

quantitative assessment of the biological impact and evidence of stream recovery (case study 3.12). 

Stressor ID/CADDIS

In 2000 EPA’s Office of Water and ORD developed a process for identifying any type of stressor or 

combination of stressors that causes biological impairment. The Stressor Identification Guidance 

Document (USEPA 2000a) is intended to lead water resource managers through a formal and rigorous 

process that identifies stressors causing biological impairment in aquatic ecosystems and provides a 

structure for organizing the scientific evidence supporting the conclusions.

The SI process is prompted by biological assessment data indicating that a biological impairment has 

occurred. The general SI process entails critically reviewing available information, forming possible stressor 

scenarios that might explain the impairment, analyzing those scenarios, and providing conclusions about 

which stressor(s) are causing the impairment. The SI process is iterative, usually beginning with a 

Purpose: To identify the cause of aquatic life impairment when a waterbody is listed because of 

biological impairment and the cause is unknown.

This tool can be used to answer questions such as the following: 

• How can I use biological and stressor information to identify cause of biological 

impairment?

Sources: Stressor Identification Guidance Document (USEPA 2000a); EPA’s CADDIS website: 

http://www.epa.gov/caddis
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 23

retrospective analysis of available data. The accuracy of the identification depends on the quality of data 

and other information used in the SI process. In some cases, additional data collection might be necessary 

to accurately identify the stressor(s). The conclusions can be translated into management actions, and the 

effectiveness of those management actions can be monitored (Figure 2-4). 

The core of the SI process consists of the following three main steps:

 Listing candidate causes of impairment. 

 Analyzing new and 

previously existing 

data to generate 

evidence for each 

candidate cause. 

 Producing a causal 

characterization 

using the evidence 

generated to draw 

conclusions about 

the stressors that 

are most likely to 

have caused the 

impairment. 

Again, the SI process is 

iterative. Practitioners will 

begin by analyzing available 

data to see if sufficient 

information is already 

available. The kinds of 

information needed include 

information on the type of 

impairment, the extent of 

the impairment, any 

evidence of the usual 

causes of impairment

(e.g., hydrologic alteration, invasive species, habitat loss, toxicants, total nitrogen and phosphorus), and 

other information from the site. The evidence is considered first and then other, less direct kinds of 

evidence are gathered and evaluated, if needed. For example, one might consider other situations that 

are similar and can provide useful insights.

CADDIS is an online application of the SI process that uses a step-by-step guide, worksheets, technical 

information, and examples to help scientists and engineers find, access, organize, share, and use 

environmental information to evaluate causes of biological effects observed in aquatic systems such as 

streams, lakes, and estuaries.14 CADDIS also contains updates, clarifications, and additional material 

developed since the SI guidance document was published in 2000.

 

14 http://cfpub.epa.gov/caddis/index.cfm. 

Source: USEPA 2010b

Figure 2-4. Stressor identification process.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 24

Case Example: Nutrient Management in the Little Miami River, Ohio

In the early 1980s, Ohio EPA designated the Little Miami River as an Exceptional Warmwater 

Habitat (EWH) following the first complete biological survey of the mainstem and key tributaries 

in the Ohio WQS under the new system of tiered aquatic life uses adopted in 1978. While not all 

sites sampled in 1983 attained the EWH biological criteria for both the fish and macroinvertebrate 

assemblages, sufficient sites did attain the EWH use, thus demonstrating the potential for 

attainment of that use as long as critical habitat were present.

In 1988, more stringent effluent limits for typical wastewater treatment plant (WWTP) 

parameters (e.g., biochemical oxygen demand [BOD], ammonia-N, common heavy metals) were 

established for municipal WWTPs. In 1993, as part of the Ohio EPA rotating basin approach, both 

water quality and biological improvements were observed, accompanied by increase in waters 

achieving the EWH use. These improvements resulted from water quality-based permitting at 

municipal WWTPs and compliance with more stringent effluent limits. However, suburban 

development in the surrounding communities resulted in increased WWTP flows and loads 

through the 1990s and the level of stress on aquatic systems increased. In 1998 biological 

assessment results again documented a decline in EWH attainment. The decline was associated 

with increased phosphorus loadings, which had not been targeted as part of the earlier water 

quality-based permitting. Additionally, increased diel dissolved oxygen variations and elevated 

phosphorus concentrations were observed. Following a determination that the observed 

degradation was related to loadings discharged primarily during summer low flows (i.e., from 

municipal WWTPs), the largest WWTPs implemented a phased reduction of phosphorus loadings 

through NPDES permits.

A follow-up biological assessment in 2007 documented attainment of the EWH biological criteria

along most of the mainstem of the Little Miami River after point source phosphorus controls were 

implemented. The findings documented the effectiveness of the nutrient removal provided by the 

WWTPs and confirmed the original hypothesis that the biological impairments were indeed linked 

to phosphorus loadings discharged by the point sources. This example highlights the value of 

conducting before-and-after biological assessments to support NPDES permitting. 

Source: Ohio EPA (Environmental Protection Agency). 2009. Biological and Water Quality Study of 

the Lower Little Miami River and Selected Tributaries 2007 Including the Todd Fork Watershed. 

Watershed assessment units 05090202 06, 07, 08, 09 and 14. Clermont, Clinton, Hamilton, and 

Warren counties. Ohio EPA technical report EAS/2009-10-06. 201 pp.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 25

Case Example: Causal Assessments of Impairment in Iowa

The Iowa Department of Natural Resources (IDNR) identified causes of biological impairment of 

the Little Floyd River using EPA’s SI methodology (Haake et al. 2010). Through its biological 

monitoring program and using Iowa’s benthic macroinvertebrate index, IDNR identified the Little 

Floyd River as impaired, with biotic index scores well below the reference population for the area. 

IDNR applied the SI process to biological, chemical, and physical data collected from the river.

Candidate causes for the biological impairment were flow alteration, substrate alteration, 

turbidity, altered basal food source, low dissolved oxygen concentrations, high temperature, and 

high ammonia concentrations. Biological metrics specific to the impairment were used to identify 

a less impaired location in the stream to help discover the cause of more severe effects in other 

parts of the stream. These paired biological, physical, and chemical data from the stream were 

used to develop evidence of co-occurrence of exposure and effects and evidence of preceding 

causation; that is, the presence of sources and mechanistic pathways leading to conditions where 

exposure could occur. Evidence that the exposure level was sufficient to cause either the fish or 

the invertebrate effects was developed from two Iowa data sets with paired biological, physical, 

and chemical data. The interquartile range of values for the various stressors from ecoregion 

reference sites were compared to the values observed for the Little Floyd River. Also, the mean 

value at statewide random sites was compared to the values in the Little Floyd River. All the 

supporting or discounting evidence was weighted, and the body of evidence for each candidate 

cause was weighed.

The formal process revealed that sediment deposition, hypoxia, heat stress, and ammonia toxicity 

were probable causes of impaired biological condition in the Little Floyd River. Other causes were 

discounted if they were unlikely or deferred if the data were insufficient to make a determination. 

The assessment was used to develop a recovery plan for the stream and was a contributing 

impetus for developing temperature criteria as part of IDNR’s WQS. Without Iowa’s basic 

commitment to integrated monitoring and use of biological, physical, and chemical data, the 

analysis and the SI would not have been possible.

Source: Haake, D.M., T. Wilton, K. Krier, A.J. Stewart., and S.M. Cormier. 2010. Causal assessment 

of biological impairment in the Little Floyd River, Iowa, USA. Human Ecological Risk Assessment

16(1):116–148.
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October 2011 26

Chapter 3. Case Studies

Biological assessments, in conjunction with other data (chemical, toxicity, physical, landscape), provide

water quality management programs the data and information necessary to document the effectiveness 

of management actions to protect and restore water quality and to clearly communicate that

information to the public. Biological assessment data, WET test results, and physical and chemical 

monitoring are used to build the relationship between the stressors being managed and the biological 

impact of the stressors. By relating biological condition to the level and type of stress, results of 

individual program actions can be related to a common measure of actual environmental 

improvements—the condition of the aquatic biota (Figure 3-1). The ultimate goal is a water quality 

management program that integrates biological, physical, and chemical data to create a more complete 

picture of resource conditions that supports effective implementation of the NPDES and TMDL 

programs.

Figure 3-1. Biological data and assessments support integrated decision making. 

By quantifying the stressor-response relationships, it is possible to explain to stakeholders the effects on 

aquatic life. For example, biological assessment data can be used to document the effects on aquatic life 

from an undetected toxic effluent from a point source, increasing impervious surfaces in a watershed, 

the loss of wetlands, or the effects of channelization. Once management actions are implemented, 

biological assessment data can measure the biological benefits of addressing those effects. That

information helps the public understand what is being protected or what could be restored and whether 

state or tribal water quality standards (WQS) (i.e., aquatic life protection) are being met. Typically, with 

improved understanding of what is at stake, the public is more informed, motivated, and engaged in 

working with the state/tribal or local agencies in setting goals for protection or restoration and 

designing solutions that work.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 27

Over the past four decades, state and tribal water quality programs have used technical tools and 

information on biological condition to support management decisions. Development of practical 

methods and technical approaches for biological assessment programs includes field testing by state 

and tribal programs. These technical advancements build upon existing approaches and can be used by 

states and tribes to strengthen their biological assessment and biological criteria programs. This chapter 

presents 17 examples of how states and tribes have incorporated such information and tools into their 

programs or are exploring additional biological condition applications.

The case studies are listed below.

Case Studies

3.1 Protecting Water Quality Improvements and High Quality Conditions in Maine

3.2 Arizona’s Development of Biological Criteria

3.3 Protection of Antidegradation Tier II Waters in Maryland

3.4 Using Complementary Methods to Describe and Assess Biological Condition of Streams in 

Pennsylvania 

3.5 Use of Biological Assessments to Support Use Attainability Analysis in Ohio

3.6 Screening Tool to Assess Both the Health of Oregon Streams and Stressor Impacts

3.7 North Fork Maquoketa River TMDL in Iowa

3.8 Addressing Stormwater Flow in Connecticut’s Eagleville Brook TMDL for Biological 

Impairment

3.9 Vermont’s Use of Biological Assessments to List Impaired Waters and to Support NPDES

Permit Modification and Wastewater Treatment Facility Upgrades 

3.10 Restoration of Red Rock Creek by the Grand Portage Band of Lake Superior Chippewa

3.11 Using Biological Assessment Data to Show Impact of NPS Controls in Michigan

3.12 Using Biological Assessment as Evidence of Damage and Recovery Following a Pesticide 

Spill in Maryland and the District of Columbia

3.13 Support for Dredge and Fill Permitting in Ohio

3.14 Virginia INSTAR Model for Watershed Protection

3.15 Examination of Climate Change Trends in Utah

3.16 Applications of Biological Assessment at Multiple Scales in Coral Reef, Estuarine, and 

Coastal Programs

3.17 Partnerships in the Protection of Oregon’s Coho Salmon
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3.1 Protecting Water Quality Improvements and High Quality Conditions in Maine

In 1983 the Maine Department of Environmental Protection (ME DEP) initiated a statewide biological 

monitoring and assessment program and revised water quality standards (WQS) by 1986 to recognize 

high levels of water quality condition. Maine established four classes for freshwater rivers and streams 

(see Table 3-1). All four classes meet or exceed the Clean Water Act (CWA) section 101(a)(2) goal for 

aquatic life protection. Every waterbody is assigned to one of four tiers by considering its existing 

biological condition, its highest achievable condition on the basis of biological potential, aquatic habitat, 

watershed condition, levels of dissolved oxygen, and numbers of bacteria (Table 3-1). Agency biologists 

developed a linear discriminant model to measure the biological attainment of each class, establish 

numeric biological criteria, and assign corresponding antidegradation tiers for purposes of statewide 

planning (see Table 3-1, column 6). Part of Maine’s antidegradation policy requires that where any 

actual measured water quality criterion exceeds that of a higher class, that quality must be maintained 

and protected [Maine Revised Statutes Title 38, §464.4(F)]. In effect, by having multiple levels of aquatic 

life use standards in law, Maine has established a means of improving water quality in incremental 

steps, and of using antidegradation reviews and reclassification upgrades to maintain and protect water 

quality and aquatic life conditions that exceed existing or designated aquatic life uses. 

The following case study offers an example of how Maine has used tiered use classifications and 

antidegradation policy cooperatively in its water quality management program. In conjunction with 

habitat and other chemical and physical parameters, Maine assigns waters to designated use classes 

(AA, A, B, or C; Table 3-1) on the basis of the potential for water quality improvement. In the 1980s, 

monitoring on the Piscataquis River near the towns of Guilford and Sangerville found aquatic life 

conditions insufficient to meet even the minimum Class C conditions at which the river was classified. 

The segment of the river in the Guilford-Sangerville area had a history of poor water quality, including 

recurrent fish kills from poorly treated industrial and municipal wastes. However, the state determined 

that this segment of the river could attain at least Class C. The state determined that sewage treatment 

plant and industrial discharges were the only significant source of stressors to the river, with very good 

quality upstream conditions and good salmonid production elsewhere. Additionally, the river’s habitat 

structure and hydrologic regime were very good.

Abstract

Maine has used biological, habitat, and other ecological information to designate aquatic 

life uses that reflect the highest achievable conditions of its waterbodies and has used 

antidegradation policy to maintain and protect high existing conditions. Maine uses a 

Biological Condition Gradient to designate levels of protection for its waterbodies (e.g., 

designated aquatic life uses) and to assign numeric biological criteria to protect those uses. 

Maine describes the system as a tiered use classification. For Maine, tiered aquatic life uses 

highlight the relationship between biology, water quality, and watershed condition in 

determining the need for waterbody protection to maintain existing high quality conditions or 

the potential for water quality improvement to attain water quality standards. Maine’s 

integrated, data-driven approach has resulted in documented improvement in water quality 

throughout the state, including upgrades of designated uses of more than 1,300 stream miles, 

from Class C to Class B, and from Class B to Class A or AA waters (Outstanding National 

Resource Waters). 
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October 2011 29

Table 3-1. Criteria for Maine river and stream classifications and relationship to antidegradation 

policy. 

Class

Dissolved 

oxygen 

criteria

Bacteria 

criteria

Habitat 

narrative 

criteria

Aquatic life narrative criteria*** and 

management limitations/restrictions

Corresponding 

federal 

antidegradation 

policy tiers

AA As naturally 

occurs

As 

naturally 

occurs

Free-flowing 

and natural

As naturally occurs**; no direct 

discharge of pollutants; no dams or 

other flow obstructions. 

3 (Outstanding 

National 

Resource Water 

[ONRW])

A 7 ppm; 75% 

saturation

As 

naturally 

occurs

Natural** Discharges permitted only if the 

discharged effluent is of equal to or 

better quality than the existing quality 

of the receiving water; before issuing a 

discharge permit the Department shall 

require the applicant to objectively 

demonstrate to the department’s 

satisfaction that the discharge is 

necessary and that there are no 

reasonable alternatives available. 

Discharges into waters of this class 

licensed before 1/1/1986 are allowed to 

continue only until practical alternatives 

exist.

2 1/2

B 7 ppm; 75% 

saturation

64/100 

mg (g.m.) 

or 

236/100 

ml (inst.)*

Unimpaired** Discharges shall not cause adverse 

impact to aquatic life** in that the 

receiving waters shall be of sufficient 

quality to support all aquatic species 

indigenous** to the receiving water 

without detrimental changes to the 

resident biological community.**

2 to 2 1/2

C 5 ppm; 60% 

saturation; 

and

6.5 ppm 

(monthly 

avg.) when 

temperature 

is </= 24 °C 

125/100 

mg (g.m.) 

or 

236/100 

(inst.)*

Habitat for fish 

and other 

aquatic life

Discharges may cause some changes to 

aquatic life**, provided that the 

receiving waters shall be of sufficient 

quality to support all species of fish 

indigenous** to the receiving waters 

and maintain the structure** and 

function** of the resident biological 

community. **

1 to 2

Source: Maine DEP (modified). http://www.maine.gov/dep/blwq/docmonitoring/classification/reclass/appa.htm.

Notes:

* g.m. = geometric mean; inst. = instantaneous level. 

** Terms are defined by statute (Maine Revised Statutes Title 38, §466). 

*** Numeric biological criteria in Maine regulation Chapter 579, Classification Attainment Evaluation Using 

Biological Criteria for Rivers and Streams.
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Four years after issuance of new National Pollutant Discharge Elimination System (NPDES) permits 

requiring better industrial pretreatment and improved wastewater treatment at the Guilford-Sangerville 

treatment facility, follow-up monitoring found water quality improvements that exceeded Class C and 

attained Class B aquatic life conditions. The achievement of higher water quality conditions was 

preserved through a classification upgrade process (supported by the industry and the two towns). The 

river was upgraded to Class B and now attains those higher aquatic life use goals. The redesignation 

process requires the state legislature to enact a statutory change of a waterbody’s classification and can 

take considerable time to complete. However, during the reclassification process the improved water 

quality conditions existing in the Piscataquis River were protected through implementation of the state’s 

Tier II antidegradation policy. The value secured by maintaining the higher quality condition was 

demonstrated in 2009 when the Piscataquis River was designated as critical habitat for the restoration 

of the endangered Atlantic salmon.

The management actions based on documented improvements in the biological condition in this 

example demonstrate the complementary application of the state’s tiered aquatic life use classification 

and the Tier 2 and 21⁄2 antidegradation policy. Using that approach, water quality upgrades from Class C 

to B and from B to A or AA have been repeated in many parts of the state, and subsequently maintained 

and protected. Overall, Maine has redesignated more than 1,300 miles of streams to a higher class on 

the basis of biological information (e.g., biological improvements due to point source controls, nonpoint 

source practices, dam operational modifications or removal) and societal values (e.g., water quality and 

habitat protection for wild trout populations; critical species protection, especially Atlantic salmon 

habitat and tribal petitions). 
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3.2 Arizona’s Development of Biological Criteria

Development of Numeric Biological Criteria

Arizona began a biological assessment program in 1992, following EPA’s Rapid Biological Assessment

Protocols for wadeable streams and rivers (Plafkin et al. 1989). Standard operating procedures for 

macroinvertebrate monitoring in perennial, wadeable streams and for laboratory processing and 

taxonomic identification were established and have been periodically reviewed and updated (ADEQ 

2010). A statewide reference monitoring network was established to develop an index of biological 

integrity (IBI) as the macroinvertebrate assessment method.

A classification analysis was first performed on the statewide macroinvertebrate data set to identify 

regions of statistically different macroinvertebrate communities across the state (Spindler 2001).

Elevation-based regions were the result of the classification analysis, consisting of two broad 

macroinvertebrate regions and community types:

 A warmwater community below 5,000 feet elevation

 A coldwater community above 5,000 feet elevation

All wadeable, non-effluent-dependent perennial streams in the regions, with some documented 

exceptions, are predicted to have the same general macroinvertebrate community type. IBIs were then 

developed for both a warmwater and coldwater community using the statewide reference site data 

(ADEQ 2007).

In the initial stages of development, Arizona’s numeric biological criteria were based on the idea that 

the structure and function of aquatic benthic macroinvertebrate communities provide information on

the overall quality of their surface waters and on attainment of the state’s designated aquatic life uses. 

Measuring the composition and structure of the biological communities in minimally disturbed surface 

waters provides reasonable approximation of biological integrity and, thus, the basis for establishing the 

reference condition (Stoddard et al. 2006). The reference condition provides the benchmark for 

evaluating the biological condition of surface waters that could have been subjected to relatively greater 

amounts of disturbance.

However, on the basis of the state’s scrutiny of the reference site database and further investigation of 

surrounding land use, the state concluded that its reference sites represent best available, or least 

disturbed, conditions for each watershed. There was uncertainty as to whether some of the reference 

sites at the lower range of the reference distribution were truly minimally disturbed conditions. For 

example, while reference sites were in a wilderness area for streams considered to be in pristine 

Abstract

Arizona has adopted in its water quality standards both narrative and numeric biological 

criteria to help protect aquatic life uses in wadeable, perennial streams designated for either 

coldwater aquatic and wildlife or warmwater aquatic and wildlife. The biological criteria allow 

the state to define expected conditions relative to reference streams. The state implements a 

two-step verification process to confirm attainment of the biological criteria for waters that 

score just below the attainment threshold. Arizona Department of Environmental Quality uses 

the biological assessment results in its 305(b) reports on the condition of its aquatic resources.
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October 2011 32

condition, much of the watershed upstream was extensively grazed, and the index scores for the 

reference sites were lower than the mean. In addition, there was variability because of sites later found 

to be intermittent in flow, and samples were affected by extreme flooding in the reference data set. 

Because of that uncertainty in reference quality in the low end of the reference database, Arizona 

selected the 25th percentile of the reference site distribution to be protective of the aquatic life use.

Arizona established a two-stage process for determining nonattainment of the numeric biological criteria. 

On the basis of statistical analysis of reference, stressed, and test data sets, an attainment threshold of 

25 percent was selected. The nonattainment biological criteria threshold was set at the 10th percentile of 

reference, the level at which a majority of stressed samples occurs in the Arizona Department of 

Environmental Quality (ADEQ) database. An inconclusive zone falls between the 10th and 25th percentiles 

of reference. The zone of uncertainty encompasses variability in IBI scores near the 25th percentile. To 

verify the biological integrity of the inconclusive samples, verification sampling is required before making 

an attainment decision. Verification monitoring must be conducted during the next immediate spring or 

fall index period. (A fall-based IBI scoring system is being developed.) If the waterbody in question scores 

at or less than the 25th percentile of reference, it will then be judged as not attaining. Such a verification 

approach provides an opportunity to confirm the status of waters that score just below the attainment 

threshold of the biological criteria.

Adoption of Numeric Biological Criteria 

On January 31, 2009, Arizona adopted biological criteria, as part of the revised Arizona surface water 

quality standards (WQS), applicable to wadeable, perennial streams with either a coldwater or 

warmwater designated aquatic life use. The biological criteria consist of two parts: a narrative statement 

(Arizona R18-11-108) and numeric criteria (ARS R18-11-108.01). The narrative is presented as follows: 

A wadeable, perennial stream shall support and maintain a community of organisms having a taxa 

richness, species composition, tolerance, and functional organization comparable to that of a stream 

with reference conditions in Arizona.

The numeric criteria are laid out in text and numeric form (Table 3-2) in the state’s biological criteria rule 

in the WQS as follows:

The biological standard in R18-11-108(E) is met when a biological assessment result, as measured by 

the Arizona IBI [index of biological integrity], for cold or warm water is: 1) Greater than or equal to 

the 25th percentile of reference condition, or 2) Greater than the 10th percentile of reference 

Minimally Disturbed Condition: The physical, chemical, and biological conditions of a waterbody 

with very limited human disturbance compared with natural, undisturbed conditions. There might 

be some changes to the composition of the resident aquatic biota, but native species are present.

Least Disturbed Condition: The best existing physical, chemical, and biological condition of a 

waterbody affected by human disturbance. These waters have the least amount of human 

disturbance in comparison to others within the waterbody class, region, or basin. Least disturbed 

condition is a relative term, and the actual condition may depart significantly from natural, 

undisturbed conditions or minimally disturbed conditions. Least disturbed condition might change 

significantly over time as human disturbances change.
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October 2011 33

condition and less than the 25th percentile of reference condition and a verification biological 

assessment result is greater than or equal to the 25th percentile of reference condition.

Table 3-2. Arizona numeric biological criteria IBI scores

Biological assessment result

IBI scores

coldwater warmwater

Greater than or equal to the 25th percentile of reference condition > 52 > 50

Greater than the 10th and less than the 25th percentile of reference 

condition

46–51 40–49

Source: Arizona R18-11-108.01

ADEQ uses the biological assessment results in its 305(b) reports on the condition of its aquatic 

resources. More information about the biological criteria, sampling methods, establishing reference 

condition, and the method for determining nonattainment of the biological criteria is provided in

Biocriteria Implementation Procedures (ADEQ 2008) and in Technical Support Documentation for the 

Narrative Biocriteria Standard (ADEQ 2007).
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3.3 Protection of Antidegradation Tier II Waters in Maryland

In its state water quality standards (WQS), Maryland adopted an antidegradation policy for protecting all 

waters for existing and designated uses. High-quality (Tier II) waters receive additional attention and 

regulatory protections. Identification of Tier II waters, in this case streams, is based on a waterbody-bywaterbody approach using biological survey data, from which two indices of biotic integrity (IBIs) are 

developed—one for benthic invertebrates and one for fish. Those with both scores above 4 are 

designated Tier II waters. The state has identified more than 230 high-quality water segments. To 

protect downstream high-quality waters, a watershed approach to protection is applied. Tier II waters 

must be protected so that water quality does not degrade to minimum standards, and that requirement 

has implications for potential discharges and local planning activities. 

Application of Tier II Protection

The Maryland Department of the Environment (MDE) requires that applicants for amendments to 

county plans (i.e., water and sewer plans) or permits for new or expanding point source discharges 

evaluate alternatives to eliminate or reduce discharges or impacts [COMAR 26.08.02.04-1(B)]. 

Applicants for permits must consider whether the receiving waterbody is Tier II (or whether a Tier II 

determination is pending); MDE reviews proposed amendments to county plans discharging to Tier II 

waters. In both cases, discharges to Tier II waters require a Tier II review [2.26.08.02.04-1(F)]. 

MDE has developed a cooperative approach to protecting Tier II waters. Monitoring and WQS programs 

work with the National Pollutant Discharge Elimination System (NPDES) permitting program to help 

screen for potential effects from new or expanded discharges and to develop permit conditions to 

minimize those effects and maintain existing high-quality waters. Outreach materials are available to 

educate county planners about Tier II waters, and geographic information system (GIS) shapefiles that 

planners can use to help locate Tier II waters within their jurisdictions have been developed.

15 That

information provides Maryland county planners a way to determine early on whether their projects 

could affect Tier II waters.

 

15 More information about GIS is at http://www.gis.com/content/what-gis. 

Abstract

Maryland is identifying high-quality waters for antidegradation purposes on a waterbodyby-waterbody basis. Maryland has designated Tier II waters on the basis of two indices of 

biotic integrity—fish and benthic invertebrates—and provides additional protection so that 

those waters are not degraded. New or increased point source dischargers and local sewer 

planning activities that have the potential to affect Tier II waters are required to examine 

alternatives to eliminate or reduce discharges or impacts. The state has developed 

requirements that must be met for projects that do not implement a no-discharge 

alternative. To help local planners to determine whether a planned activity has the potential 

to affect a Tier II water, the state has developed geographic information system shapefiles 

that identify such waters. Those files are provided to local jurisdictions to improve their 

knowledge of where Tier II waters occur. Biological assessments, in conjunction with 

chemical and physical assessments, are then conducted to determine the status of those 

waters and detect trends in condition.
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A list of recommendations for land-disturbing projects that are not able to implement a no-discharge 

alternative provides the following initial guidance: 

1. Implementation of environmental site design (also known as low-impact development)—Design 

elements and practices must be approved for Tier II waters with opportunity provided for 

exploration of appropriate alternatives and justification for structural elements in the proposed 

designs.

2. Expanded riparian buffers—Buffers must be at a minimum of 100 feet; wider buffers may be 

required depending on slope and soil type.

3. Biological, chemical, and flow monitoring in the Tier II watershed—Applicants may be required 

to conduct biological assessments in conjunction with chemical, physical, and flow assessments

to help determine the remaining assimilative capacity and cumulative impacts of current and 

future development. Depending on project specifics, additional monitoring may be required, 

such as the completion of a hydrogeologic study for a major mining project or additional pH 

monitoring because of impacts associated with instream grout applications seen in many 

common transportation projects.

4. Additional practices—Depending on the potential for project-specific effects on water quality, 

applicants may be required to implement other practices, such as enhanced sediment and 

erosion control practices or implementation of more environmentally protective alternatives. 

If those general requirements cannot be implemented, applicants must submit a detailed hydrologic 

study and alternatives analysis to demonstrate that the assimilative capacity of a waterbody will be 

maintained. The assimilative capacity of a waterbody is typically site-specific and determined through 

studies of the waterbody. In terms of WQS, assimilative capacity is a measure of the capacity of a 

receiving water to assimilate additional pollutant(s) but still meet the applicable water quality criteria 

and designated uses.
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3.4 Using Complementary Methods to Describe and Assess Biological Condition 

of Streams in Pennsylvania

Describing Waters along a Gradient of Condition

Pennsylvania Department of Environmental Protection 

(PA DEP) has developed a new benthic 

macroinvertebrate index of biotic integrity (IBI) for the 

wadeable, freestone (high-gradient, soft-water) streams 

in Pennsylvania using the reference condition approach 

(PA DEP 2009). PA DEP has alternative assessment 

methods in place for other stream types (i.e., lowgradient pool-gliders, karst [limestone]-dominated). The 

IBI provides an integrated measure of the overall 

condition of a benthic macroinvertebrate community by 

combining multiple metrics into a single index value. 

PA DEP uses the IBI to assess attainment of aquatic life 

uses. 

Additionally, PA DEP is exploring use of a Biological 

Condition Gradient (BCG) to describe the biological 

characteristics of freestone streams along a gradient of 

condition. PA DEP conducted a series of three expert 

workshops in 2006, 2007, and 2008 to calibrate a BCG 

along a gradient from minimally to heavily stressed 

conditions (PA DEP 2009). The BCG is a narrative model 

based on measurable attributes, or characteristics, of 

aquatic biological communities expected in natural 

conditions (e.g., presence of native taxa, some pollution 

tolerant taxa present but typically not dominant, 

absence of invasive species). Additionally, the BCG model includes attributes that describe interactions 

among biotic communities (e.g., food web dynamics), the spatial and temporal extent of stress, and the 

presence of naturally occurring habitats and landscape condition (for more information, see Tool # 2,

The Biological Condition Gradient). To date, states and tribes that have applied the BCG have used the 

BCG attributes that describe the taxonomic composition of the resident aquatic biota and, where 

Abstract

The Pennsylvania Department of Environmental Protection (PA DEP) has developed a new 

benthic macroinvertebrate index of biotic integrity (IBI) to assess the health of wadeable, 

freestone (e.g., high gradient, soft water) streams. Additionally, PA DEP calibrated a benthic 

macroinvertebrate Biological Condition Gradient (BCG) and is exploring using the BCG to 

more precisely describe biological characteristics in Pennsylvania streams. Potentially, the 

BCG can be used in conjunction with the IBI to identify aquatic life impairments and to 

describe the biological characteristics of waters assigned special protection. PA DEP is also 

exploring using a discriminant analysis model with additional taxonomic, habitat, and 

landscape parameters to describe exceptional value waters.

A metric is a measurable aspect of a 

biological community that responds in a 

consistent, predictable manner to 

increasing anthropogenic stress.

Examples of metrics include taxa 

richness, which is a measure of the 

number of different kinds of organisms 

(taxa) in a sample collection, and

% dominance, which is a measure of 

which species compose the majority of 

organisms present in a sample 

collection.

To gain a more comprehensive view of 

an aquatic community, multiple types 

of metrics are combined into a 

biological, or biotic, index. The typical 

biological index may include 

information from 7 to 12 different 

metrics. The metric values are typically 

scored on a unitless scale of 0 to 100 

and averaged to obtain a single value.
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October 2011 37

available, information on fish condition, for example lesions and abnormalities (BCG attributes I–VII)

(see Table 2-2). Some states are exploring the application of additional attributes on food web dynamics, 

extent of stress, and landscape condition (BCG attributes VIII–X). These efforts are providing valuable 

information that will aid the U.S. Environmental Protection Agency (EPA) in further refining the BCG.

To develop the BCG for its streams, biologists from PA DEP, in conjunction with external taxonomic 

experts and scientists, e.g., the Delaware River Basin Commission, Western Pennsylvania Conservancy,

and EPA, used the BCG attributes that characterize specific changes in community taxonomic 

composition (PA DEP 2009). For example, in the highest tiers of the BCG, locally endemic, native, and 

sensitive taxa are well represented (attributes I and II) and the relative abundances of pollution-tolerant 

organisms (attribute V) are typically lower. With increasing stress, more pollution-tolerant species may 

be found with concurrent loss of pollution-sensitive species (attribute VI). At the beginning of the expert 

workshops, the biologists first assigned or adjusted BCG attributes to each macroinvertebrate taxon 

(e.g., pollutant-sensitive or tolerant) and then reviewed taxa lists from samples representing minimally 

disturbed to severely disturbed site conditions (Figure 3-2). The evaluated samples included sites judged 

as either reference quality (e.g., at or close to minimally disturbed conditions) or heavily stressed based 

on specific selection criteria (PA DEP 2009). To further test the robustness of the BCG process, additional 

sites that were not part of the reference or heavily stressed sample groups were evaluated. Those sites 

represented a range of site conditions, including moderately to heavily stressed site conditions (nonreference and moderately stressed; see Figure 3-2). Using the BCG tier descriptions of predicted changes 

in the attributes as a guide, they assigned each site to one of the six BCG tiers.

Figure 3-2. Comparison of calibrated BCG tier assignments (mean value) and IBI scores for freestone streams 

representing range of conditions from minimal to severely stressed.
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For all the evaluated samples, PA DEP biologists analyzed the relationship between a sample’s BCG tier 

assignment with its corresponding IBI score (PA DEP 2009). A strong correlation existed between the 

calibrated BCG tier assignments and the IBI scores (Figure 3-2). Based on these results, PA DEP is 

evaluating using the BCG to describe the biological characteristics of streams along a gradient of 

condition; for example, the reference sites clustered at IBI scores near 80 and above. Based on 

taxonomic information and without knowledge of the IBI scores, the experts assigned these sites to BCG 

tiers 1.5 to 2.5. BCG tier 2 represents close to natural conditions (e.g., minimal changes in structure and 

function relative to natural, or pristine, conditions; supports reproducing populations of native species 

of fish and benthic macroinvertebrates). This information can meaningfully convey to the public the 

biological characteristics of waters in the context of the Clean Water Act and the goal to protect aquatic 

life. Using both the IBI and BCG, PA DEP might be able to develop a cost-effective, publicly transparent 

approach to routinely monitor and assess the condition of its freestone streams and to help identify 

potential high-quality (HQ) or exceptional value (EV) streams.

Describing Exceptional Value Waters

Pennsylvania’s regulations define waters of EV that are of unique ecological or geological significance.

EV streams are given the highest level of protection and constitute a valuable subset of Pennsylvania’s 

aquatic resources. To support protection of these waters, PA DEP is considering the use of a discriminant 

analysis model to evaluate the relationship between condition of the watershed, a stream, and its 

aquatic biota (e.g., the connection of riparian areas with a stream and the floodplain or the spatial 

extent of stressors and their sources in the watershed). PA DEP is evaluating the use of a discriminant 

model that incorporates measures of land use and physical habitat along with IBI scores and indicator 

taxa richness to make distinctions between EV and HQ waters. The abiotic measures PA DEP is using 

address habitat fragmentation and spatial and temporal extent of stress and are comparable to the 

national BCG model attributes IX (extent of stress) and X (ecosystem connectance). The results of this 

effort could potentially support decisions on where to target resources for sustainable, cost-effective 

protection of EV waters and healthy watersheds. Through this work, PA DEP is providing EPA valuable 

feedback on the technical development and potential program application for BCG attributes IX and X.

Potential Application to Support Protection of Waters of Highest Quality

PA DEP is exploring new approaches to help identify streams that are of the highest quality and might 

require special protection. For example, a stream might be found to meet the expected biological 

condition of an HQ or EV water based on its IBI score and BCG tier assignment. This information could be 

used to support further study to determine whether its designation should be as an HQ water or if it 

meets the additional criteria for designation as an EV water. When biological information is presented in 

context of a BCG framework, it is easier for the public to understand the status of the aquatic resources, 

including waters that are in excellent condition and require additional protection. 
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3.5 Use of Biological Assessments to Support Use Attainability Analysis in Ohio

In 1990 Ohio used biological assessment information to specify levels of biological condition for specific 

streams and rivers based on ecoregional reference sites. As a result, the state refined definitions of 

some aquatic life uses, adopted new ones, and assigned biological criteria to key uses to support a tiered 

approach to water quality management within the Ohio water quality standards (Table 3-3).

Table 3-3. Summary of Ohio’s beneficial use designations for the protection of aquatic life in streams. 

Beneficial use designation Key attributes

Coldwater habitat (CWH) Native cold water or cool water species; put and take trout stocking.

Exceptional warmwater habitat (EWH) Unique, unusual, and highly diverse assemblage of fish and 

invertebrates.

Seasonal salmonid habitat (SSH) Supports lake run steelhead trout fisheries.

Warmwater habitat (WWH) Typical assemblages of fish and invertebrates, similar to least impacted 

reference conditions.

Limited warmwater habitat (LWH) Temporary designations based on 1978 WQS. Predate Ohio tiered 

aquatic life use classification and were not subjected to UAA; being 

phased out as UAA are conducted for each LWH waterbody or segment. 

Most of the LWH waterbodies or segments have been redesignated as 

WWH or higher with the exception of some mine-drainage-affected 

segments that were designated LRW.

Modified warmwater habitat (MWH) More tolerant assemblages of fish and macroinvertebrates are present 

relative to a WWH assemblage, but otherwise generally similar species

to WWH present; irretrievable modifications of habitat preclude 

complete recovery to least impacted reference condition.

Limited resource water (LRW) Fish and macroinvertebrates severely limited by physical habitat or other 

irretrievable condition; minimum protection afforded by the CWA.

Source: Ohio EPA, April 2004. http://www.epa.ohio.gov/portals/35/wqs/designation_summary.pdf. 

Abstract

Ohio uses biological assessment information in conjunction with physical habitat 

assessments to strengthen use attainability analyses (UAAs) in the state. The technical and 

programmatic underpinnings for Ohio’s use attainability determinations is the state’s

aquatic life use classification approach, which is based on the relationship between biology, 

habitat, and the potential for water quality improvement. Ohio’s biological monitoring and 

assessment program provides timely, statewide information on the status of waterbodies 

and the data to support a UAA if needed, including when biological conditions improve and 

an upgrade of a designated use is warranted. Typically, in situations where the habitat 

needed to meet aquatic life uses is present, Ohio has taken management actions to address 

water quality issues and restore impairments. 
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When designating aquatic life uses, the quality of habitat is a major factor in a use attainability analysis

(UAA) process to determine the potential for restoration and expected biological condition for streams 

and rivers in Ohio. If sufficient good habitat attributes are not present, such as higher quality substrates 

and sufficient instream cover, a determination about restorability is made. If habitat is sufficient or 

could be restored, it is assumed that any observed biological impairments are due to the effects of other 

stressors (e.g., metals, nutrients) that could be remediated through readily available water quality 

management options (e.g., permit conditions and/or best management practices [BMPs]) and the 

biological assemblage restored. The aquatic life use classifications are based on ecological conditions, 

and in 1990 biological criteria were developed to protect each use. Ohio’s biological criteria include two 

indices based on stream fish assemblages (Index of Biological Integrity [IBI] and Modified Index of WellBeing [MIwb]) and one index based on stream macroinvertebrate assemblages (Invertebrate 

Community Index [ICI]). The biological criteria were developed based on regional reference conditions 

and are stratified by each of the state’s five level 3 ecoregions and three site types (headwater, 

wadeable, and boatable sites). 

Using these aquatic life use classifications, Ohio has been able to determine attainable levels of 

condition for streams and rivers. For example, in the mid-1980s biological surveys of Hurford Run, a 

small stream located in an urban/industrial area of Canton, Ohio, showed that the stream was severely 

impaired by toxic chemical pollutants and that some sites had no fish at all. Hurford Run is channelized 

for nearly its entire length. Because of the severity of the biological impairment, a UAA was conducted 

to determine if the warmwater habitat (WWH) aquatic life use was attainable and, if not, to determine 

the most appropriate designated use for the stream. Based on biological and habitat assessments, the 

most appropriate aquatic life uses for the different segments of Hurford Run could be determined. For 

example, very poor habitat quality from historical channelization in the upper reach of Hurford Run and 

the associated hydrological modifications (e.g., ephemeral flows) resulted in a limited warmwater 

habitat (LWH) designation for this upper reach.

The middle reach of Hurford Run has been subject to extensive, maintained channel modifications that 

also resulted in degraded habitat features, though water is always present. Channel maintenance 

practices resulting in poor-quality substrates, poorly developed pools and riffles, and a lack of instream 

cover preclude biological recovery to assemblages consistent with the WWH use, which indicated that 

the middle reach should be designated a modified warmwater habitat (MWH), reflecting the attainable 

biological potential for a channel-modified stream determined by scientific studies. The lower reach of 

Hurford Run was previously relocated and channelized, but over time the reach has naturally recovered 

sufficient good-quality habitat attributes, such as coarse substrates and better developed riffle and pool 

features associated with the WWH use for this ecoregion. Biological assessments confirmed the 

presence of aquatic assemblages typical of WWH. Based on this information, this segment was 

designated as WWH. The designated aquatic life uses reflect the current best possible condition in each 

segment of Hurford Run and provide a basis for management actions to ensure that the associated 

criteria are met and the use is protected. Numeric biological criteria have been established for key

designated aquatic life uses, and a segment is listed on the 303(d) list if it is in nonattainment of the 

biological criteria. Additionally, the different segments are routinely monitored by the state and the 

condition reevaluated on a regular basis. If there is any information indicating that a higher use is being 

attained or could be attained, that water is considered for redesignation to the higher use.

Ohio has also used biological assessment data to refine its water quality criteria in some cases. For 

instance, when Ohio’s aquatic life use classifications were established in 1978, Ohio established 

dissolved oxygen criteria to protect each designated use. Initially, a dissolved oxygen criterion of 6 mg/L 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 41

as a minimum was established for exceptional warmwater habitat (EWH) waters to protect highly 

sensitive species supported by this use. However, analyses of ambient biological and chemical data 

suggested that the 6 mg/L minimum criterion was over-protective for EWH waters. Data showed a 

relationship between stressors and biological measures, with dissolved oxygen concentrations less than 

5.0 mg/L being associated with IBI scores not in attainment of EWH biological criteria. And, in general, 

data showed that with dissolved oxygen greater than 5.0 mg/L, IBI scores are much more likely to attain 

EWH. These results were used to justify refining the EWH criteria to the current 6 mg/L average, 5 mg/L 

minimum (Ohio EPA 1996). The criterion revision also supported the redesignation of some rivers and 

streams from WWH to EWH.
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3.6 Screening Tool to Assess Both the Health of Oregon Streams and Stressor 

Impacts

The John Day River Basin in northeastern Oregon is one of the state’s most important scenic waterways. 

It drains nearly 8,100 square miles of land and is one of the nation’s longest free-flowing river systems 

(BLM 2010). Oregon Department of Environmental Quality (ODEQ) evaluated the biological health of 

streams in the John Day River Basin using biological sampling for macroinvertebrates. The study also 

identified the causes of stream impairment with the aid of biological monitoring information. The focus 

of the studies conducted by ODEQ was to model the biological condition and explore the relative 

importance of the two most common nonpoint source (NPS) stressors—elevated temperature and 

excess fine sediments—using macroinvertebrate data.

Biological Condition Model (PREDATOR)

ODEQ sampled benthic macroinvertebrates in 76 perennial, wadeable streams in the John Day River 

Basin. The biological condition of the streams was modeled using ODEQ’s PREDictive Assessment Tool 

for ORegon (PREDATOR) (Hubler 2008). The model predicts the kinds of macroinvertebrates expected to 

occur at reference sites with similar environmental conditions (precipitation, air temperature, elevation, 

and ecoregion). For example, high-elevation sites that experience higher precipitation levels and cooler 

air temperatures in eastern Oregon would be expected to support macroinvertebrates similar to those 

found at reference sites that are both geographically and environmentally similar.

The PREDATOR model uses 176 reference sites across five Level III ecoregions in Oregon (Omernik 

1987). The model output is the ratio of the macroinvertebrates observed at a test site (O) to the 

expected macroinvertebrates (E), or O/E. Values less than 1.0 represent a loss of reference 

macroinvertebrates at the test site relative to natural conditions. ODEQ classifies sites into one of three 

biological condition classes: least disturbed, moderately disturbed, and most disturbed. Oregon’s least 

disturbed class supports native populations of aquatic macroinvertebrates and natural habitat.

The results of the study indicated that almost half of the sites were in least disturbed conditions, or 

equivalent to reference (O/E values close to 1.0). Just over one-quarter (28 percent) were in most disturbed 

conditions with O/E values down to 0.47, indicating loss of over half of the expected, or native, species.

Abstract

The Oregon Department of Environmental Quality conducted a study in the John Day River 

Basin to both evaluate the biological health of streams using biological sampling for 

macroinvertebrates and to identify the causes of stream impairment using biological 

monitoring information. The state used the PREDATOR model to evaluate waterbody 

conditions in perennial streams. Stressor identification models were used to measure the 

effects of stress from two sources of nonpoint source pollution (excessive temperature and 

fine sediment). A comparison of modeling results to sampling data showed that both 

modeling and direct measurements are useful in identifying streams not meeting 

benchmarks and identifying cause of impairment. Oregon will continue to use the model 

results to evaluate the ability to identify causes of biological impairment on the basis of 

macroinvertebrate data and will use that information to improve water quality.
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NPS Pollutant Stressor Models

To use macroinvertebrates to measure the effects of stress from NPS pollution (temperature and fine 

sediments), ODEQ used two stressor identification (SI) models (Huff et al. 2006). Temperature stress (TS) 

and fine sediment stress (FSS) are two new biological indices used to infer seasonal maximum 

temperature and percent fine sediments based entirely on the macroinvertebrates collected at a site.

Those indices consistently and predictively respond to increased levels of temperature or fine sediments 

and are used to model macroinvertebrate-specific changes to the stressors (e.g., stressor-response 

signatures).

Comparisons of Stressor Model Output to Field Measurements

Water quality and physical habitat information was also collected as part of the John Day River Basin 

study. Direct comparisons of the SI models (assemblage response signatures) to their equivalent physical 

measurements (water column temperature and fine sediment load) show similar abilities in determining 

the extent of streams failing to meet benchmarks. However, the SI models showed a stronger 

relationship to biological condition than did the physical measurements of temperature and fine 

sediments. Most of the test sites in good condition according to the PREDATOR model coincided with 

the SI model outcomes also in good condition. The test sites in good biological condition supported 

specific macroinvertebrates with temperature and fine sediment preferences similar to reference 

assemblages. Conversely, the majority of sites in poor biological condition (most disturbed) had TS and 

FSS values above the reference benchmark for the SI model. To further identify the relative importance 

of temperature and fine sediments to biological condition, ODEQ routinely performs more quantitative 

analyses. Regression models of the relationship between PREDATOR and SI models can be used to 

identify the strength and significance of relationships. Additionally, relative risk analysis is used to 

quantitatively rank the importance of stressors to biological condition.

Conclusions 

ODEQ developed two SI models that can be used to identify the relative importance of two common 

NPS stressors–– elevated temperatures and fine sediments––to biological condition. ODEQ’s primary 

objective with the analysis was to explore the ability of macroinvertebrate data to identify causes of 

biological impairment.

The results from the study show that about one-half of the perennial, wadeable streams in the John Day 

River Basin are in good condition, one-quarter are in fair condition, and one-quarter are in poor 

condition. SI models were used to identify primary causes of biological impairment from NPS pollution. 

Although biological measures and physical measures were comparable in their ability to detect the 

extent of sites with NPS stressors above levels typically observed at reference sites, the biological 

measures showed a stronger relationship to biological condition.

The models for biological condition and SI show promise as sensitive and cost-effective screening tools 

for detecting NPS impairment to streams and targeting best management practices (BMPs) to address 

the primary stressors, elevated temperature and excessive fine sediment loads. The SI models also 

provide benchmarks to measure the response of the biological community to BMP implementation. 

Combining the information from the models can help scientists better understand the risks associated 

with NPS pollution in Oregon streams and more efficiently target resources to improve water quality.
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 44

Complementary Application of Biological Condition and Stressor Identification Models:

An Example

Biological Condition: North Fork Deer Creek had a list of 14 expected macroinvertebrate taxa that 

were frequently observed at reference sites with similar geographical and environmental 

characteristics. However, only nine of the expected taxa were observed at the sampling site, 

resulting in a rating of most disturbed condition (O/E = 9/14 = 0.64).

Stressor Identification: The SI models were used to infer temperature and fine sediment 

conditions using the tolerances and abundances of all macroinvertebrates collected at North Fork 

Deer Creek. The dominant macroinvertebrates in the creek showed high tolerances to fine 

sediments, while the same taxa showed preferences for cooler water over warmer water. For 

example, five taxa were indicators (taxa that exhibit strong preferences) of higher fines at a site,

compared to one indicator taxa for low fines. Additionally, five taxa were indicators of cool water 

conditions in North Fork Deer Creek, compared to one indicator taxa of warmwater conditions.

The tolerances of the most abundant macroinvertebrates observed in North Fork Deer Creek 

indicate that excess fine sediments are the most likely cause of the poor (most disturbed) 

biological condition.
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3.7 North Fork Maquoketa River TMDL in Iowa

Water Quality Impairment of the North Fork Maquoketa River

The North Fork Maquoketa River (NFMR) is designated by Iowa for aquatic life protection as a class B 

(WW-2)16 water. In 1998 the NFMR was determined not to be meeting its aquatic life uses based on 

biological assessments of the benthic macroinvertebrate population that showed low total abundance 

and species diversity and several reported fish kill events of unknown source. Iowa subsequently placed 

the 19.5-mile segment that extends from the headwaters near Luxemburg to Dyersville on its 1998 

Clean Water Act (CWA) section 303(d) list of impaired waters. The segment was listed for a biological 

impairment of “unknown causes” (IDNR no date).

Monitoring and Stressor Identification

Iowa Department of Natural Resources (IDNR) conducted additional biological monitoring of the NFMR 

between 1999 and 2005. Data collection included the number of benthic macroinvertebrates (by lowest 

practical taxon), number of fish (by species), and instream and riparian habitat assessments. IDNR used 

these data to calculate a Benthic Macroinvertebrate Index of Biotic Integrity (BMIBI) and a Fish Index of 

Biotic Integrity (FIBI) that quantify several aquatic community characteristics such as relative abundance 

of sensitive and tolerant species, and the proportion of organisms belonging to various feeding, 

spawning, or habitat classifications. BMIBI and FIBI scores for the NFMR watershed are provided in Table 

3-6. For the sites sampled, the BMIBI and FIBI ranged from poor to fair (Table 3-4). None of the BMIBI or 

FIBI scores attained the reference biological criteria (Table 3-5). Qualitative scoring guidelines for the 

BMIBI and FIBI are summarized in Table 3-4, while reference values are included in Table 3-5.

 

16 Under the CWA, class B waters are designated for the protection of aquatic life uses. The WW-2 classification is 

for small streams.

Abstract

In 1998 the Iowa Department of Natural Resources (IDNR) determined that a 19.5-mile 

segment of the North Fork Maquoketa River (NFMR) was not meeting its aquatic life use

due to a biological impairment of “unknown cause.” This determination was based on 

biological assessments of benthic macroinvertebrate and fish populations. All collected data 

were used by IDNR in the development of a stressor identification (SI) process that showed 

that the primary pollutants in the NFMR were sediment, nutrients (specifically phosphorus), 

and ammonia. In 2007 IDNR completed a Total Maximum Daily Load report for the NMFR 

that used results of the SI process and calls for steep reductions in sediment reaching the 

river and in nutrients and agricultural manure releases. IDNR also identified a variety of best 

management practices to improve water quality and is encouraging local residents and 

businesses to take action to restore their watershed.
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Table 3-4. Qualitative scoring guidelines for the BMIBI and FIBI. 

Biological Condition Rating (BCR) BMIBI FIBI

Poor 0‒30 0‒25

Fair 31‒55 26‒50

Good 56‒75 51‒70

Excellent 76‒100 71‒100

Source: http://www.iowadnr.gov/Environment/WaterQuality/WatershedImprovement/WatershedResearchData/

WaterImprovementPlans/PublicMeetingsPlans.aspx. (Note that the NFMR TMDL .pdf document is available 

under the heading “Final Water Quality Improvement Plans.”) 

Table 3-5. Reference criteria for assessing biological integrity. 

Ecoregiona BMIBI FIBI

52B Ref. (Paleozoic Plateau) 61 59

47C Ref. (Iowan Surface) 59 71 (riffle), 43 (non-riffle)

Source: http://www.iowadnr.gov/Environment/WaterQuality/WatershedImprovement/WatershedResearchData/

WaterImprovementPlans/PublicMeetingsPlans.aspx. (Note that the NFMR TMDL .pdf document is available 

under the heading “Final Water Quality Improvement Plans.”) a

 The watershed contributing to flow in the NFMR upstream from Dyersville, Iowa, is a transitional area that is 

divided between two ecological regions of Iowa. Roughly two-thirds of the lower portion of the watershed is 

located in the Iowan Surface of the Western Corn Belt Plains, while the upper third is located in the Paleozoic 

Plateau (Driftless Area) ecoregion.

Table 3-6. BMIBI and FIBI results for the NMFR Watershed. 

(BCR rating in parenthesis)

Site Year BMIBI FIBI

REMAP 147 2005 42 (Fair) 34(Fair)

TMDL 28 2001 47 (Fair) 29 (Fair)

TMDL 28 2005 26 (Poor) 37 (Fair)

New Wine Park 1999 N/Aa 32

TMDL 29 2001 47 (Fair) 26 (Fair)

TMDL 30 2001 51 (Fair) 33 (Fair)

TMDL 30 2005 48 (Fair) 7 (Poor)

H2 1999 53 (Fair) 37 (Fair)

Modified from http://www.iowadnr.gov/Environment/WaterQuality/WatershedImprovement/

WatershedResearchData/WaterImprovementPlans/PublicMeetingsPlans.aspx. [Note that a new link to the Web 

page where the NFMR TMDL .pdf document is available under heading “Final Water Quality Improvement 

Plans.”] a

 Insufficient numbers of organisms for BMIBI calculation. To calculate the BMIBI, at least 1 of 3 quantitative 

benthic macroinvertebrate sample replicates must contain 85 or more individual specimens. The three replicates 

had 70, 25, and 54 specimens, respectively. 

In addition to biological monitoring, IDNR also collected monthly water quality samples in 2001 and 

2005 (March through November) for several chemical and physical parameters, such as flow, dissolved 

oxygen, temperature, pH, nitrate + nitrite, and total phosphorus. The data showed water quality impacts 

relative to levels measured at least disturbed ecoregion reference stream sites—especially elevated 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 47

concentrations of ammonia, nitrate-nitrogen, total phosphorus, and total suspended solids. Occasional 

violations of dissolved oxygen criteria were found, and large diurnal fluctuations in dissolved oxygen 

concentrations in the stream were indicative of elevated primary production levels. All collected 

biological, chemical, and physical data were used in the stressor identification (SI) process (IDNR 2006). 

IDNR staff followed the Protocol for SI to determine the cause of the biological impairment in NFMR (see 

Tool # 3, Stressor Identification (SI) and Causal Analysis/Diagnosis Decision Information System 

(CADDIS)). The SI procedure relates impairments described by biological assessments to one or more 

specific causal agents (pollutants). It also separates water quality (pollutant) impacts from habitat 

alteration impacts. Although the SI did not reveal any single stressor that is clearly the dominant cause

of biological impairment, IDNR determined that the primary pollutant-related causal factors in the 

NFMR were sediment, nutrients (specifically phosphorus), and ammonia.

Total Maximum Daily Load Development 

In 2007, IDNR completed Total Maximum Daily Loads for Sediment, Nutrients, and Ammonia: North Fork 

Maquoketa River, Dubuque County, Iowa. Results of the SI process were used, and IDNR considered 

impacts from the point and nonpoint sources of pollution in development of the Total Maximum Daily 

Load (TMDL). Although IDNR concluded that one wastewater treatment plant in the NFMR watershed 

should be included in the TMDL and in developing a wasteload allocation for the existing phosphorus 

load, that facility did not contribute significantly to the overall sediment load. IDNR also identified 

several potential nonpoint sources for nutrients, sediment, and ammonia—failed on-site septic tank 

treatment systems, agricultural activities (e.g., cattle in streams, fertilizer use, soil erosion, land-applied 

manure), wildlife, and runoff from developed areas (IDNR 2007). 

To meet water quality improvement goals for the NFMR, the TMDL includes a 77 percent reduction in 

sediment reaching the river (20,200 pounds of sediment per year) and a 73 percent reduction in 

nutrients and manure releases. The TMDL has two parts. The first includes setting specific and 

quantifiable targets for sediment, oxygen demand, total phosphorus, and ammonia loads to the stream. 

Additional biological and water quality monitoring will determine whether the prescribed load 

reductions result in attainment of water quality standards. These monitoring data will also be used to 

determine whether the implemented TMDL and watershed management plans have been effective in 

addressing water quality impairments in the NFMR. EPA approved the IDNR TMDL in 2008.

IDNR has identified a variety of BMPs to improve water quality, as well as to encourage residents and 

businesses in the watershed to take action. IDNR has also identified possible practices to reduce 

sediment and nutrients reaching the NFMR, such as installing structures to reduce both agricultural and 

urban runoff; limiting cattle access to streams and installing alternative water sources for cattle; and 

using agricultural management practices that increase crop residue, such as no-till. IDNR also suggested 

that proper control of open agricultural animal feedlots will help prevent contaminated runoff from 

reaching streams, which in turn will reduce ammonia loading. Ongoing monitoring of this impaired 

stream segment will be used to periodically assess progress made toward attainment of the NFMR

designated aquatic life uses.

 
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3.8 Addressing Stormwater Flow in Connecticut’s Eagleville Brook TMDL for 

Biological Impairment

Eagleville Brook has a 2.4-square-mile drainage area, and the watershed drains a portion of the 

University of Connecticut (UCONN) campus and the town of Mansfield. The brook is designated as a 

Class A waterbody, but fisheries sampling in 2002 showed that the waterbody was not meeting its 

aquatic life uses, with low fish density and large areas with no fish. Additionally, benthic 

macroinvertebrate sampling in 2003 showed low total abundance and species diversity, documenting 

that the waterbody was in nonattainment of the state’s narrative biological criteria for Class A waters. In 

2004 Connecticut added Eagleville Brook to its list of impaired waters for cause unknown on the basis of 

the biological assessment results. 

Stressor Identification and Total Maximum Daily Load Development 

Before Total Maximum Daily Load (TMDL) development, Connecticut conducted a stressor identification 

(SI) analysis to evaluate the potential stressors and determine the most likely causes of impairment. The 

SI study concluded that biological impairments were most likely from a combination of pollutants 

related to stormwater runoff from developed areas and other related stressors (such as the physical 

impacts of stormwater flows). There are no other known point source discharges in this small 

watershed. The major source of stormwater is runoff from the impervious surfaces in the watershed 

(e.g., roads in Mansfield and UCONN campus). A statewide study of the impact of impervious cover (IC) 

on aquatic habitats was also conducted; Connecticut’s Rapid Biological Assessment Protocol III data 

from 125 small (< 50 square miles) watersheds showed that no stream monitoring location with more 

than 12 percent IC in the upstream watershed meets Connecticut’s biological criteria for full support of 

aquatic life use.

In 2007 Connecticut developed the TMDL with a loading capacity (TMDL target) of 12 percent IC. The 

12 percent TMDL target was chosen on the basis of the threshold observed for applicable Connecticut

streams in the statewide study. In the TMDL, Eagleville Brook was partitioned into three segments, and 

the IC was calculated for each. For each segment, a TMDL implementation objective was also developed 

(Table 3-7).

Abstract

In 2004 Connecticut used biological assessment information to place Eagleville Brook on its 

303(d) list of water quality limited (WQL) waters for failure to meet the brook’s aquatic life 

uses. Before Total Maximum Daily Load (TMDL) development, the state conducted a

stressor identification analysis that pointed to the complex array of pollutants transported 

by stormwater as the most likely cause of impairment. A statewide study that correlated 

impervious cover (IC) with benthic macroinvertebrate data collected from wadeable 

streams was conducted, and results showed that the designated aquatic life use was not 

supported when IC was more than 12 percent of the watershed area. A TMDL was 

developed in 2007 using a target of 12 percent IC—the first in the nation to use IC as a 

surrogate for stormwater. Objectives to reduce IC were established for each waterbody 

segment, and progress toward attainment of the designated aquatic life use will be 

evaluated by monitoring the condition of the benthic macroinvertebrate community in 

conjunction with ongoing chemical assessments.
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Table 3-7. Summary of TMDL analysis for Eagleville Brook. 

Waterbody segment TMDL target IC Implementation objective

From the mouth at Eagleville Pond upstream to 

the confluence with Kings Brook, Mansfield

12% 5% Antidegradation

The confluence with Kings Brook to headwaters 

near UCONN campus

12% 14% 21% reduction in the percent IC

Unnamed pond on UCONN campus 12% 27% 59% reduction in the percent IC

The targets apply at all times (instantaneously, daily, monthly, seasonally, and annually) and will achieve 

reductions in stormwater runoff volume in all storm events whenever they occur (e.g., on any day) 

throughout the year. The reductions associated with the implementation objectives were to be 

accomplished by improved stormwater management. The Connecticut Department of Environmental 

Protection (CT DEP) provided general and specific implementation recommendations in the TMDL and 

recommended using an adaptive management approach toward reducing stormwater impacts and 

improving water quality.

TMDL Implementation

Progress toward attainment of the aquatic life use will be evaluated by CT DEP’s monitoring the 

macroinvertebrate and fish communities and assessing surface water chemistry according to an existing 

rotating basin sampling schedule. UCONN, the Town of Mansfield, and the Willimantic River Alliance 

have pledged support for TMDL implementation. EPA and CT DEP have funded a project using section 

319 NPS funds to map locations and identify ways to reduce the effect of IC as required by the TMDL. 

The project also examined the estimated costs of such actions and developed initial engineering 

sketches for a top ten list for recommended retrofit management actions that are most cost-effective, 

primarily in the upper watershed. In addition, other projects have been completed on the UCONN 

campus to reduce IC, including installation of two green roofs and parking lots with pervious asphalt and 

concrete. The Town of Mansfield has received technical guidance on local land use regulations and 

practices, primarily in the lower watershed. Low-impact development concepts are expected to be 

incorporated into future development. An overall watershed management plan that supports a 

framework to pursue high-priority projects to reduce the effect of IC has been developed. Considerable 

stakeholder input has crafted a consensus approach to seize opportunities to reduce the effect of IC as 

situations arise during normal maintenance operations at UCONN and Mansfield. A tiered system to 

track progress will focus in the short term on close tracking of the area of new and disconnected IC, as 

well as flow monitoring to determine whether changes in IC will improve the hydrologic regime of 

Eagleville Brook. The TMDL has led to an increase in dialog among stakeholders and has led to changes 

in how people think about managing IC in the Eagleville Brook watershed. Additional information on the 

implementation of the Eagleville Brook TMDL can be found at 

http://clear.uconn.edu/projects/tmdl/index.htm.This site, hosted by UCONN, provides additional 

information and will be used to track the progress of TMDL implementation over time.
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3.9 Vermont’s Use of Biological Assessments to List Impaired Waters and to 

Support NPDES Permit Modification and Wastewater Treatment Facility 

Upgrades

Biological Assessments Detect Impairment and Support Permit Modifications

Between 1993 and 1995, biological assessments of Vermont’s Dog River showed that the river was not 

meeting its aquatic life use according to changes in the aquatic community typically associated with 

toxicity stress and moderate phosphorus pollution. In 1996, Vermont Department of Environmental 

Conservation (VT DEC) listed the Dog River on the state’s 303(d) list of impaired waters, based on the 

biological assessment information, for cause unknown. Further investigation indicated two factors 

contributing to the degraded instream water quality. First, the Northfield Wastewater Treatment Facility 

(WWTF) had reached its design life and was no longer able to function properly and reliably meet 

National Pollutant Discharge Elimination System (NPDES) permit limits. Second, wastewater influent to 

the facility from two industrial textile facilities had high concentrations of metals and possibly 

surfactants. In WWTF effluent samples, metal concentrations were high and predicted to exceed water 

quality criteria at permitted flows. Whole effluent toxicity (WET) testing confirmed significant toxic 

effects at effluent concentrations greater than 12 percent. Through a toxicity identification evaluation 

(TIE) study, copper was identified as the most significant metal of concern in the WWTF effluent, with a 

maximum copper concentration of 184 micrograms per liter (μg/L). This level would have resulted in an 

instream concentration of 36 μg/L copper at 7Q10 (i.e., the lowest 7-day, consecutive low flow period 

occurring over the preceding 10-year period) permitted flows. Copper levels correlated with the level of 

toxicity found in the WET testing.

In 1999 pretreatment discharge permits with compliance schedules were issued to the textile facilities. 

The pretreatment permits established copper limitations for those influent waste streams that required 

the installation of pretreatment systems for the removal of copper (see Table 3-8). Although the systems 

were operational in 2000, biological assessments conducted between 2000 and 2003 showed continued 

aquatic life use impairment in the river. That monitoring showed a shift in the benthic 

macroinvertebrate community that, in addition to chemical data, indicated that phosphorus pollution 

had become the most likely cause of the aquatic life impairment. Specifically, the macroinvertebrate 

community was significantly higher in density and dominated by nutrient-tolerant taxa relative to 

previous sampling results. To measure this increase in nutrient-tolerant taxa, VT DEC used a ratio that 

compares the proportion of pollution- sensitive benthic macroinvertebrate species to more pollutanttolerant species, the EPT/EPTc ratio. This reflects the ratio of generally pollution-sensitive species (e.g., 

Ephemeroptera [mayflies], Plecoptera [stone flies] and Trichoptera [caddisflies]) compared to the more 

pollutant-tolerant species (Chironomids [midges/flies]). A low threshold indicates dominance of midges 

Abstract

In the 1990s, the Vermont Department of Environmental Conservation’s biological 

assessment of the Dog River showed aquatic life use impairments downstream of a 

wastewater treatment facility. Whole effluent toxicity and biological assessment data were 

used to support revisions to National Pollutant Discharge Elimination System permits for 

dischargers, and subsequent management actions at the facilities resulted in the segment’s 

meeting its designated aquatic life use and its removal from the 303(d) listing for water 

impairment.
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October 2011 51

(EPTc) that have been observed in streams with significant levels of nitrogen, phosphorus, or other 

pollutants. Additionally, the higher biological index value reflected the increase in the midges and 

provides complementary information. 

Table 3-8. Permit limitations for two textile facilities. 

Facility

Flow

monthly average

Copper

Monthly average Daily maximum

Facility A 150,000 gal/day 0.027 lb/day 0.038 lb/day

Facility B 35,000 gal/day 0.007 lb/day 0.0125 lb/day

In January 2003, VT DEC issued a compliance schedule to the Village of Northfield to upgrade its WWTF, 

and the upgraded facility became operational in November 2004. The upgraded WWTF process consists 

of upgraded headworks, two sequential batch reactors, a surge tank, and an upgraded chlorination and 

dechlorination system. Phosphorus removal was required to comply with the requirements of the Lake 

Champlain TMDL and Vermont regulations (10 VSA 1266a). To achieve that, permit limits for a 1.0-

mg/day discharge of phosphorus were set at 6.78 lb/day, at concentration of 0.8 mg/L monthly average. 

Northfield treatment plant copper effluent limitations were also established at 0.26 lb/day monthly 

average and 0.36 lb/max daily at a pH of between 6.5 and 8.5. Improved sludge management was also 

incorporated into the upgraded WWTF, including refurbishing the existing digester, adding a new 

digester, and adding a centrifuge for dewatering. Water quality and habitat improvements were 

observed, but the aquatic system’s recovery was further complicated by a chlorine spill from the 

WWTF’s temporary disinfection system during the upgrade in July 2004, leading to a further short-term 

decline in EPT.

Conclusion 

Despite the short-term adverse effects from the 2004 chlorine spill, the compliance schedules and 

changes to both predischarge and the WWTF permits have resulted in changes in facility operations 

that, in turn, have resulted in improvements in water quality. Biological assessments showed 

improvement only after copper was reduced and wastewater treatment of phosphorus was improved.

These combined efforts enabled a site that was classified as fair-poor to recover to excellent condition. 

Biological assessments in 2005 and 2006 showed that the Dog River was meeting its aquatic life uses, 

with specific measures, or metrics, showing density to be moderate; richness, EPT, and EPT/EPTc ratio to 

be high; and biological index (BI) to be lower relative to previous sampling. Chemical monitoring has 

documented that the applicable chemical water quality criteria were being met, and WET test results 

have shown that the effluent is nontoxic (i.e., no significant toxicity to test organisms using 100 percent

effluent). The biological assessment information documents that the stream macroinvertebrate 

community is now dominated by water-quality-sensitive taxa more typical of its natural expectation—

with recovery of sensitive species and a more balanced community. (Data from sampling between 1993 

and 2006 are shown in Table 3-9.) As a result, in 2006 Vermont removed Dog River from its impaired 

waters list. 
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Table 3-9. Macroinvertebrate assessments for Dog River—Northfield WWTF. 

Date 1993 1994 1995 2000 2001 2003 2004 2005 2006

Assess 

(criteria)

Fair Fair Fair Fair-Poor Poor Poor Poor Very 

Good

Excellent

Density 

(> 300)

1,862 3,282 1,037 4,556 5,640 4,264 668 2,160 5,870

Richness 

(> 30)

39 43 41 50 50 62 34 51 62

EPT 

(> 18)

12 16 16 14 11 22 12 28 33

BI 

(< 5.00)

4.73 4.74 4.61 5.51 6.00 5.26 5.12 4.38 3.48

Ept/EptC 

(> 0.45)

0.029 0.50 0.52 0.29 0.07 0.22 0.14 0.89 0.89

Milestones:

2000 – Metals removed. 

2004 – Chlorine spill late summer; WWTF upgrade with phosphorus removal completed in November. 

2005 – First year of river meeting designated aquatic life use. 

2006 – Second year of river meeting aquatic life use; stream removed from impaired waters listing.
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3.10 Restoration of Red Rock Creek by the Grand Portage Band of Lake Superior 

Chippewa

Background 

Over the past decade, the Grand Portage Band of Lake Superior Chippewa (tribe) has been leading 

restoration efforts to improve the physical, chemical, and biological integrity of one of the Band’s 

impaired waters—Red Rock Creek. To date, biological assessment information has played a central role 

in defining biological goals for restoration in concert with chemical and physical targets that have also 

been established. The tribe has implemented restoration activities that have resulted in water quality 

improvements, as shown in sampling of both the benthic macroinvertebrate and plant communities.

Red Rock Creek Impairment 

The Red Rock Creek watershed encompasses approximately 1,200 acres in Minnesota north of Lake 

Superior. While the upper reaches of the watershed are in relatively pristine condition, the creek flows 

through an abandoned gravel pit located approximately one-half mile from Lake Superior. Past gravel 

mining activities—most notably the removal of riparian (streamside) vegetation and cutting of a portion 

of the stream bank—have adversely affected the stream, resulting in severe sedimentation. This has 

resulted in a net loss of fish species and benthic macroinvertebrate communities. For instance, by 2006, 

steelhead trout, chinook salmon, coho salmon, and coaster brook trout were found only near the mouth 

of the stream, rather than their previous habitation along several miles of the stream. Gravel extraction 

has also caused the stream to leave its former channel and to spread into the gravel pit area. Notably, 

beaver damming has exacerbated problems associated with braiding and flow and has led to clogging of 

Red Rock Creek. 

Monthly sampling of Red Rock Creek began in 1997. Turbidity measurements were high, with a mean 

concentration of 12.3 nephelometric turbidity units (NTUs). Gravel mining activities ceased in 1998, and 

in 2000 the Tribe reported that water quality was impaired based on biological and chemical 

assessments. Specifically, monitoring showed low dissolved oxygen concentrations, high turbidity, and 

low benthic macroinvertebrate densities and species abundance. In the impacted portion of the creek, 

mean dissolved oxygen concentrations were 6.3 mg/L—more than 2 mg/L lower than the 

concentrations measured in unimpacted upstream reaches. A total of27 macroinvertebrates were 

collected in the impacted stream reach, with a large proportion of pollution/sediment-tolerant diptera 

(e.g., Chironomides [midges]) present but no pollution-sensitive EPT taxa (e.g., Ephemeroptera 

[mayflies], Plecoptera [stone flies] and Trichoptera [caddisflies])). However, in 2004, 6 years after the 

cessation of gravel mining operations, over 100 macroinvertebrates were collected. Possible 

explanations for this improvement in macroinvertebrate density might be the subsequent regrowth of 

Abstract

For the past 15 years, the Grand Portage Band of Lake Superior Chippewa (tribe) has led 

efforts to restore one of the Band’s most impaired waters—Red Rock Creek. Biological 

assessment information has played a central role in establishing and assessing whether 

biological, chemical, and physical targets for restoration are being met. To date, the tribe 

has implemented multiple and interrelated restoration activities that have resulted in 

significant water quality improvements, as demonstrated by periodic sampling of the 

creek’s benthic macroinvertebrate and plant communities.
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October 2011 54

some of the stream’s riparian buffer and instream habitat (Table 3-10). However, only 27 percent of the 

total taxa were EPT taxa, which is much lower than the 60–75 percent proportion of EPT taxa expected 

in unimpacted or minimally impacted streams in this area. Increases in EPT taxa are expected with 

continued restoration and allowing time for the aquatic system to recover natural flow and habitat 

conditions.

In addition to benthic macroinvertebrates, the tribe also assesses plant communities to evaluate the 

biological health of its waterways. To measure the natural quality of the area, the tribe uses a Floristic 

Quality Index (FQI),17 a weighted species richness index that can be calculated by identifying all plant 

species in a given plot or transect. To evaluate streams, the Grand Portage Tribe uses an FQI score ≥ 20, 

the presence of at least 20 plant taxa, no exotic invasive plant species, and at least 5 sensitive or rare 

plant taxa. In 2004, Red Rock Creek had a total of 13 plant taxa, an FQI score of 14, 3 invasive exotic 

plant species, and no sensitive or rare plant taxa (Table 3-11). 

Restoration Efforts

The tribe set biological, chemical, and physical goals for improving overall water quality in Red Rock 

Creek (Table 3-10). Restoration goals were established for increased dissolved oxygen concentrations, 

reduced turbidity, reduced diptera taxa to less than 5 percent of macroinvertebrates collected, and 

increased proportion of pollution-sensitive macroinvertebrate taxa. Restoration efforts began in 2006 

with the removal of the beaver dam and installation of sediment traps. Monitoring results conducted 

immediately following restoration showed a mean turbidity concentration of 10.3 NTUs, dissolved 

oxygen concentrations that continued to be approximately 2 mg/L less than those in undisturbed 

reaches of the stream, and changes in the benthic macroinvertebrate community. Although sampling of 

the macroinvertebrate community showed a dramatic increase in the number of organisms collected 

(350), only 9.8 percent of the total insects collected were EPT taxa and 22 percent were diptera—similar 

to pre-restoration sampling results. In 2008 additional restoration measures were completed, including 

reinforcement of banks upstream of the sediment basin using live fascines and stakes, physical removal 

of excess sediment from the basin, and seeding and tree planting to further stabilize the banks and 

restore riparian vegetation.

Results 

Monitoring results from 2008 and 2009 show that the restoration goals for Red Rock Creek have been 

exceeded for most biological, chemical, and physical measures of water quality (Tables 3-10 and 3-11).

Dissolved oxygen concentrations and turbidity levels are comparable to those expected in unimpacted 

conditions with improvements in both benthic and floristic assessments of biological condition, though 

the continued presence of invasive plant species remains a challenge. The tribe will continue to maintain 

the sediment ponds and bank stabilization projects in order to achieve the restoration goal for percent 

EPT taxa. Regular removal of excess sediment from the basin, efforts to reestablish native vegetation in 

the riparian zone, and potential removal of invasive species from the basin will be considered in an 

adaptive management approach to fully achieve biological restoration goals.

 

17 Anthropogenic stressors can be manifest changes in plant communities through displacement and competition 

from exotic invasive species. The FQI is the calculation of the plant communities’ mean coefficient of conservatism 

multiplied by the square root of the number of species. The coefficient of conservatism is a measure of an 

individual species’ fidelity to natural habitats and communities.
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October 2011 55

Table 3-10. Sampling to assess progress toward restoration goals. 

Parameter

Pre-restoration sampling 

results (year) Restoration goal

Post-restoration sampling 

results (year)

Turbidity 12.3 NTU (1997) 50% reduction 2.4 NTU (2009)

Dissolved oxygen 6.3 mg/L (2000) 2 mg/L increase 9.6 mg/L (2009)

Number of 

macroinvertebrates

27 (2000)

10 (2004)

200 350 (2008)

% diptera 29.6% (2004) Reduction to 5% of total 1.3% (2008)

% EPT species 27% (2004) Increase to 60% of total 30% (2009)

Table 3-11. Plant sampling results. 

Parameter 2004 2008

Number of plant taxa 13 21

FQI score 14 19

Number of invasive plant species 3 3

Number of sensitive or rare taxa 0 3
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3.11 Using Biological Assessment Data to Show Impact of NPS Controls in 

Michigan

Background 

Carrier Creek, a tributary to the Grand River, flows through a rapidly developing area in Eaton County 

near Lansing, Michigan. Historical channelization and more recent urban runoff resulted in eroding 

stream banks, high sedimentation rates, and degraded aquatic habitat for fish and macroinvertebrate 

communities. In 1996 Michigan included a 4-mile segment of the creek—from its confluence with the 

Grand River upstream to where it flows under Interstate 496—on its 303(d) list of impaired waters

based on biological assessment information used to interpret its narrative standard that all surface 

waters of the state are “designated for and shall be protected for ... aquatic life and wildlife.” The 

Michigan Department of Environmental Quality (MDEQ) determined that the quality of the aquatic biota 

in that segment of the creek was reduced by urban runoff, poor instream habitat, and excessive 

sediment deposition. MDEQ completed a Total Maximum Daily Load (TMDL) for Carrier Creek biota in 

2002. As noted in the TMDL, achievement of the water quality standards (WQS) for designated uses for 

Carrier Creek will be demonstrated by assessing the macroinvertebrate community and the instream 

habitat as it relates to sediment.

Stream Restoration

Between 2000 and 2006, state and local agencies and volunteer groups partnered in various stream 

restoration projects designed to achieve the TMDL goals. For example, in 2000 local agencies and 

volunteers stabilized and restored 5 miles of channel. The projects increased channel stability, improved 

instream habitat, and reconnected the channel to its floodplain. The upstream end of the channel was 

narrowed, and the stream pattern was reestablished to promote meandering. In some locations, the 

project team removed dredge spoils that were separating the stream from its natural floodplain.

In 2002 project partners created a 32-acre wetland in the headwaters of the watershed to intercept 

stormwater runoff and decrease stream flashiness. In 2004 the Perrin Chapter of Trout Unlimited 

installed structures along the creek to provide shelter and resting points for fish. In addition, the Eaton 

County Drain Commissioner is enhancing stormwater detention and flow control throughout the upper 

portion of the watershed to stabilize the channel, reduce the velocity of the flow, reduce erosion 

downstream, and reduce the amount of flooding. That work is ongoing.

Abstract

In the 1990s biological assessments of Carrier Creek in Eaton County, Michigan, showed that 

the waterbody was not attaining its designated aquatic life uses, resulting in its inclusion on 

the state’s 303(d) list in 1996 for cause unknown. Subsequent surveys indicated that stream 

biota was affected by urban runoff, poor instream habitat, and sediment deposition. In 2002 

a Total Maximum Daily Load for biota was completed. Watershed partners are conducting 

several stream restoration projects to improve aquatic life use attainment. The restoration 

activities stabilized the stream channel and its hydrology, reduced stream bank erosion, and 

improved aquatic habitat. Improvements in fish and macroinvertebrate communities have 

been documented.
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Results 

Biological assessment data have been used to assess the project’s progress. The State of Michigan and 

the Eaton County Drain Commission collected data on fish, macroinvertebrates, and aquatic habitat 

quality at two locations in the project area, both before (2000) and after (2006) the restoration activities 

occurred. A consultant for the Eaton County Drain Commission collected additional fish data in 2007.

As of 2006, aquatic habitat was unchanged at one site and had improved at the other, but 

macroinvertebrate populations had not responded. However, by 2009, both macroinvertebrate and 

habitat quality scores had improved at all sites. The improvement in habitat scores was due to 

continued stream restoration activities that provided meandering channels and suitable instream 

habitat for the aquatic biota, such as fish and benthic macroinvertebrates. In fact, the 2007 fish data 

show that the number of fish taxa increased at both locations following restoration activities, more than 

doubling at one site and quadrupling at the other. There is another encouraging signal of improvement 

to date: a single slippershell mussel (Alasmidonta viridis) was found during an informal inspection of the 

restored reach in 2007. The slippershell is listed on the state’s threatened list by the Michigan Natural 

Features Inventory and had not been observed in the stream before restoration. MDEQ will conduct 

further monitoring in the fall of 2011.

The restoration activities conducted to date have stabilized the stream channel and its hydrology, 

reduced stream bank erosion, and improved aquatic habitat. Fish communities are recovering, and 

future monitoring should show further improvements in the biota and eventually result in removing 

Carrier Creek from the list of impaired waters based on assessing the macroinvertebrate community and 

the instream habitat as it relates to sediment.
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3.12 Using Biological Assessment as Evidence of Damage and Recovery 

Following a Pesticide Spill in Maryland and the District of Columbia

Problem Overview

In the spring of 2000 a fish kill (estimated to be 150,000 fish) was observed along an 8-mile stretch of 

Rock Creek, a major tributary of the Potomac River in Maryland and the District of Columbia. 

Responding to the kill, the Maryland Department of the Environment (MDE) sampled the water column 

and sediments and found high concentrations of the insecticides cypermethrin and bifenthrin, both of 

which are highly toxic to fish. Concentrations were especially high in a storm drain entering the stream 

from the parking lot of a pest control company, suggesting that a pesticide spill had occurred.

The case was investigated by EPA's Criminal Investigation Division with assistance from the State of 

Maryland, Montgomery County, the National Park Service, and the District of Columbia. Within 2 weeks, 

a coordinated, multiagency effort sampled sediments, fish, and benthic macroinvertebrates upstream 

and downstream of the outfall. Fish sampling was repeated after 5 months, and sediments were 

retested 9 months after the spill.

Data Collection and Analysis

Samples were analyzed in three time frames––before the spill occurred, just after the fish kill was 

observed, and some months afterward. Samples were also categorized by location; before and upstream 

samples served as controls for the suspected effects of the spill. Several hours after the fish kill was first 

observed, cypermethrin and bifenthrin concentrations in downstream waters were near the acute 

toxicity thresholds for fish and invertebrates. Pesticide concentrations in the storm drain were many 

times greater than the acute toxicity levels. Sediments tested 2 weeks after the fish kill showed elevated 

levels of cypermethrin and bifenthrin below the storm drain when compared to levels above the storm 

drain. When retested 9 months later, cypermethrin and bifenthrin concentrations in all sediment 

samples were below detection limits.

Fish and benthic macroinvertebrates were collected from 11 stations, including 4 above and 7 below the 

storm drain. Several sites had been sampled before the spill in routine monitoring programs by the 

District of Columbia and Montgomery County. Historical data from 1996‒1998 were available for three 

stations below the outfall, and one site well below the spill had been sampled several times weeks 

before the spill. Just after the spill, both fish and macroinvertebrate communities showed severe 

degradation when compared to upstream controls and, for fish only, when compared to downstream 

samples taken before the kill event.

Abstract

In response to a fish kill in a tributary of the Potomac River in 2000, biological assessment 

data were used to show the impact of a pesticide spill and to document the waterbody’s 

recovery. Sampling data collected before the spill provided a baseline of the expected 

aquatic community in the waterbody. Data from biological assessments before the spill 

were compared with sampling data collected immediately after the fish kill and several 

months later. The data were used to support enforcement actions and to support criminal 

charges against the polluter.
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Decreases in numbers of fish and the number of fish species were observed, with a reduction in the fish 

index of biotic integrity at all sites below the spill. On average, 20 macroinvertebrate taxa, of 46 taxa 

found upstream, were absent from downstream sites. After 5 months, most minnow species had 

returned to the affected sites. Overall, the fish community had recovered to approximately 75 percent 

of upstream species composition.

Conclusion 

Biological assessment provided a powerful tool for documenting stream degradation and stream 

recovery following the toxic spill. Evidence was further strengthened by baseline data collected in 

routine monitoring programs. Comparison of the post-spill samples to samples taken before the spill 

provided a quantitative assessment of the biological impact and evidence of stream recovery. In 

November 2001, the owner and an employee of the pest control firm were charged with violations of 

the Clean Water Act and the Federal Insecticide, Fungicide, and Rodenticide Act. Ongoing biological 

assessments, in conjunction with bioassays and chemical and physical assessments, can assist 

enforcement agencies in assessing damage, levying fair and reasonable damage assessments on those 

proven responsible for toxic spills, and determining the rate and level of stream recovery.
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3.13 Support for Dredge and Fill Permitting in Ohio

Dredge and Fill Permitting

States use Clean Water Act (CWA) section 401 to regulate activities that might impact aquatic habitats. 

Those wanting to modify a stream in a way that will result in the discharge of dredge or fill material into 

waters of the United States must obtain a section 404 permit from the U.S. Army Corps of Engineers and 

a section 401 water quality certification from the state. The state must certify that the proposed 

activities will comply with and not violate water quality standards (WQS) or waive such certification. 

Ohio’s designated aquatic life use classes, which are based on the relationship of habitat and the 

attendant numeric biological criteria adopted into the WQS, make that linkage a valid tool for evaluating 

the effects of habitat alterations that are covered under the CWA. In essence, the habitat tools 

employed are sufficiently predictive to serve the purpose of reviewing proposed stream habitat 

modification activities.

Ohio EPA used more than 20 years of data to develop habitat stressor gradients along several aspects of 

habitat quality at both the site and watershed scales, including overall habitat quality as measured by a 

habitat quality index, the Qualitative Habitat Evaluation Index (QHEI), and for specific attributes such as 

substrate and channel condition (Rankin 1989, 1995). This allows for sufficient predictive relationships 

such that this habitat tool can be used to help determine the attainability of the Ohio biological criteria.

Ohio’s designated aquatic life uses for surface waters have enabled a range of management responses 

to dredge and fill projects related to the quality and sensitivity of the waterbody in the context of the 

CWA goal to protect aquatic life. Ohio’s use classification system is tiered along a gradient of quality 

with the highest use class supporting pollution-sensitive, naturally occurring communities of benthic 

macroinvertebrates and fish (Exceptional Warmwater Habitat [EWH] Aquatic Life Use). A second class 

along the gradient (Warmwater Habitat [WWH]) also supports a community of pollution-sensitive, 

naturally occurring benthic macroinvertebrates and fish species that are consistent with least impacted 

reference conditions.

Nationwide permits are designed to minimize site-specific oversight where ecological risks are assumed 

to be low. Frequently, however, in reviewing the criteria where nationwide permits can apply, highquality waters can be overlooked, leading to their unwarranted alteration and impairment. Small 

streams such as headwater streams are particularly vulnerable to not being properly assessed under 

Abstract

Ohio uses biological assessments to help inform its decisions about certifying permits for 

dredge and fill activities and to ensure that the impacts of those activities on aquatic 

habitats do not violate Ohio water quality standards (WQS). Ohio’s tiered aquatic life uses, 

in conjunction with antidegradation policies and numeric biological criteria adopted into the 

state’s WQS, enable Ohio to better assess the potential impact of dredge and fill activities 

and to make management decisions on the basis of its designated aquatic life uses. Ohio’s 

designated aquatic life uses are based on the relationship of habitat and the resident biota.

It is presumed that if critical aquatic habitat is present or can be restored, the aquatic life 

associated with the habitat can be supported. Additionally, when implementing nationwide 

permits, Ohio has been able to include additional conditions to protect high-quality waters

as revealed by biological assessments. 
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nationwide permit conditions. The Ohio EWH use designation requires high-quality habitat and stable 

hydrological regimes (especially in headwater and wadeable streams). Because those essential 

attributes can be altered by direct modifications to the stream channel and other habitat features, Ohio 

requires individual reviews of projects that occur in such high-quality streams. Under a general use 

system, those sites would be lumped with all other streams under the nationwide permit system. In 

addition, antidegradation provisions for high-quality WWH and Coldwater Habitat (CWH) streams are 

also applied.

Mitigation Standards

The attention gained by biologically defined habitat impacts has prompted the development of 

mitigation standards, in conjunction with a process for rigorous validation, that will take Ohio’s aquatic 

life uses into account and require enhancement or restoration wherever feasible. The stressor-response 

relationships that have been developed between biological assemblages and key habitat attributes have 

been applied to the 401 program in Ohio for more than 20 years. For nationwide permits, a series of 

general and specific exclusions and conditions that vary with the state’s tiered uses have been derived

(USACE 2002). They include a general exclusion (of nationwide permits) for streams that are EWH and 

for certain high-quality antidegradation tiers (State Resource Waters and Outstanding State Resource 

Waters, Superior High-Quality Waters), the delineation of which was based primarily on the same 

biological assemblage attributes on which the designated use classes are based.

Ohio’s integrated approach for designating aquatic life uses, implementing antidegradation, and 

establishing biological criteria is based on relationships between the aquatic biota and critical aquatic 

habitat.
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3.14 Virginia INSTAR Model for Watershed Protection

In 2003 Virginia Commonwealth University’s Center for Environmental Studies, Virginia Department of 

Conservation and Recreation (VA DCR), the Virginia Department of Environmental Quality, Virginia 

Coastal Zone Management Program, and other state agencies began collaboration on Interactive Stream

Assessment Resource (INSTAR). INSTAR is an online, interactive database application that evaluates the 

ecological integrity of Virginia’s streams using biological assessments and habitat data. INSTAR was 

developed as part of and to support Virginia’s Healthy Waters Initiative. That initiative is an effort to 

raise awareness of the importance of stream ecological condition and how healthy it is and to make 

certain that conservation efforts are broad enough to include healthy streams and rivers, making them 

and restoration efforts a priority. The approach is complementary to water quality programs that focus 

on repairing degraded streams.

INSTAR is used to identify healthy streams using data that include information about fish and 

macroinvertebrates, instream habitat, and riparian borders. Users can access and manipulate the view 

of a comprehensive database representing more than 2,000 aquatic (stream and river) collections 

statewide. INSTAR was established to develop complementary, synoptic, and geospatial database for 

fish and macroinvertebrate community composition and abundance at stream locations throughout the 

state. INSTAR, and the extensive aquatic resources database on which it runs, supports a wide variety of 

stream assessment, management, and conservation activities aimed at restoring and protecting aquatic 

living resources throughout Virginia.

INSTAR was primarily designed as a tool that could be used for regional and local planning by providing 

support for making land use decisions and help in prioritizing stream protection and mitigation efforts. 

Advocacy groups and individuals might also want to use INSTAR to identify healthy streams in their 

communities and encourage their protection. INSTAR can support regional approaches to 

transportation, priority habitat corridor identification, greenways, zoning, and land conservation 

priorities. It can also be used to identify healthy streams vulnerable to development and those already 

protected. Locally, INSTAR can help raise awareness about the location of healthy waters and identify 

priority areas during comprehensive planning. Measures of the composition of the naturally expected 

benthic macroinvertebrate community provide a benchmark for determining a healthy stream.

INSTAR generates a Virtual Stream Assessment (VSA) score for each stream studied using data collected 

by biologists along a 150- to 500-meter length or reach of stream, depending on its width. Information 

collected includes the types and number of fish and aquatic macroinvertebrates, instream habitat 

(e.g., vegetation, rocks, fallen logs), and riparian vegetation. The information is compared statistically to 

a model reference stream that represents ideal conditions of biology and habitat for streams in that 

Abstract

The Virginia Department of Conservation and Recreation and Virginia Commonwealth 

University Center for Environmental Studies are collaborating in developing and 

implementing a statewide Healthy Waters program to identify and protect healthy streams. 

The Interactive Stream Assessment Resource (INSTAR) is an online, interactive database 

application that evaluates the ecological integrity of Virginia’s streams using biological and 

habitat data. The Web-mapping application is available to the public as a free resource to 

help planners, advocacy groups, and individuals to support wise land use decision making.
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geographic region. How closely a stream compares to an appropriate model reference stream 

determines its VSA score and ranking. That information can help identify a range of condition, from 

streams that have exceptional health to streams that are good candidates for restoration. INSTAR also 

classifies Virginia’s 1,275 small watersheds using a modified index of biological integrity (mIBI) that is 

based on occurrences of selected aquatic species found in each watershed.

With INSTAR, a user can generate stream data and mapping information at the local, regional, or 

statewide level. Searches can be done by locality, stream name, watershed, or drainage area, and 

specific locations can be pinpointed using global positioning system (GPS) coordinates or street 

addresses. Users can also access information about fish, macroinvertebrates, and habitat for a specific

stream location and can turn on topographical views, road maps, wetland overlays, and aerial photos. 

Users can also measure, outline, and highlight areas; add and edit text; and generate customized maps 

and reports. INSTAR is available to the public through a free, user-friendly website: 

http://instar.vcu.edu. 

Application of INSTAR in Richmond County

The Richmond County Local Tributary Strategy Pilot Project, funded through grants from the National 

Fish and Wildlife Foundation and VA DCR, focused on the capacity of stakeholders to develop and 

support a local program to implement statewide strategies to mitigate nutrient and sediment pollution 

delivered to local waters and the Chesapeake Bay. The project approach identified aspects of 

local/regional planning and implementation programs where consideration of strategies to meet 

regional water quality goals could lead to improved condition or improved protection of natural 

resources. The best outcome would be that implementation would affect local needs and the broader 

Chesapeake Bay goals. County-comprehensive planning and agricultural best management practice 

(BMP) implementation programs are examples of local programs that vary greatly in how they are 

managed and have regional impact. Central to success in the project was identifying a way to link such 

varied efforts so that their strategies might align with regional goals. The project worked to establish 

that link through a focus on linking land use to water quality or stream health. The link was defined by 

two data-collection efforts. A countywide INSTAR stream assessment was conducted, and a countywide 

chemical water assessment was conducted. 

The stream health assessment became a central theme for the project as the data were reviewed under 

several different contexts. 

1. The project participated in the county-comprehensive plan review and revision process as a 

partner in an extensive community engagement process. Work sessions were held to specifically 

discuss the link among land use, management and planning, stream health and natural resource 

conditions and trends, and a host of other social and economic sector interests. The stream 

health assessment was an important component of the natural resource workshop.

2. INSTAR-identified healthy stream sites were included as a component of secondary 

considerations in the local Soil and Water Conservation District Agricultural BMP Cost Share 

Program guidance.

3. The INSTAR stream assessment was used in combination with the chemical water quality and 

agricultural BMP implementation data to correlate stream health and the level of BMP 

implementation or the percentage of land treated in a site’s drainage area. The map displays an 

enhanced view of INSTAR data that includes sites identified as Important Fisheries Resources 
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and their spatial distribution against the level of BMP implementation in corresponding 

watersheds.

4. The INSTAR stream assessment was used to review the health of streams that received drainage 

from the main urbanized area affecting the county’s jurisdiction. The data allowed for 

prioritizing sites where improved stormwater management could affect local conditions and 

regional implementation goals.

5. The comprehensive nature of the stream assessment provides a baseline condition for the local 

effort to measure progress, impacts, identify threats, or conservation priorities.

The regional strategies developed under Virginia’s initial Tributary Strategies and revisited in the 

development of the Chesapeake Bay Total Maximum Daily Load (TMDL) do not provide local data to 

assist with implementation planning. The INSTAR stream assessment is a way to fill that data gap. 
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3.15 Examination of Climate Change Trends in Utah

U.S. Environmental Protection Agency (EPA) Office of Research and Development (2010c) analyzed 

biological assessment data from Utah to determine whether past climate trends could be detected and

to characterize the vulnerabilities of the biological assessment program to future climate conditions. In 

particular, the Utah Department of Environmental Quality (UT DEQ) was concerned that systematic 

changes in the physical or biological characteristics of streams would bias biological assessment scores, 

leading to errors in its integrated report. The availability of long-term stream invertebrate data at four 

reference stations, in two ecoregions, formed the basis for the analyses.

Long-term declines in richness or abundance of cold-preference taxa was detectable (i.e., from 

statistically significant temporal trends) at the two longest-term (> 15 years) Utah reference stations—

one in the Wasatch-Uinta ecoregion and the other in the Colorado Plateau. That response was 

supported by significant associations between declining richness or abundance of cold-preference 

taxa and increasing temperature. Fairly predictable losses in a metric considered sensitive to pollution 

and disturbance, EPT taxa richness, were observed with increasing temperatures at the locations, which 

represent both high- and low-elevation ecoregions. The EPT metric is a measure of the presence of 

generally pollution-sensitive species (e.g., Ephemeroptera (mayflies), Plecoptera (stone flies) and 

Trichoptera (caddisflies)) in a sample. The response of EPT taxa was largely driven by losses of 

coldwater-preference EPT taxa, but in some cases it was also influenced by gains in warm-preference 

EPT taxa.

From those results, it was estimated that a 25 - 40 percent loss of EPT taxa could occur with current 

scenarios of temperature increases by 2050 (USEPA 2010c). Should such substantial losses of EPT taxa 

due to climate change occur, it would confound measures of ecological condition and decisions 

regarding attainment of aquatic life uses in many state monitoring programs. The Utah results suggest 

that relative elevation is a contributing factor driving the temperature trait composition of regional 

benthic communities (USEPA 2010c), with a greater proportion of cold-preference taxa in the higher 

elevation ecoregions and a greater proportion of warm-preference taxa in low-elevation ecoregions.

Higher elevation regions with a greater proportion of cold-preference taxa might have a greater 

vulnerability to temperature-driven effects on traditional, taxonomically based indicators of biological 

condition. However, with the results of these studies and others, temperature-modified metrics can be 

Abstract

U.S. Environmental Protection Agency and the Utah Department of Environmental Quality 

(UT DEQ) are partnering in analysis of long-term biological assessment data to evaluate the 

potential impact of global climatic trends on the aquatic biota in Utah’s streams. UT DEQ’s 

objective is to develop a defensible approach to account for systematic bias that these 

impacts might have on its biological assessment and biological criteria program. Reference 

condition (e.g., natural or near natural condition) provides a baseline for comparison 

between expected conditions and test sites so it is important for states to understand and, 

where possible, quantify the shifts in the steady state of local reference communities due to 

global climatic shifts, regardless of whether they are natural or human-induced. For 

example, test sites should not be expected to exhibit communities that no longer exist at 

reference sites. UT DEQ’s objective is to quantify the proportion of variation attributed to 

temperature-driven effects.
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used to characterize the contribution of climate changes in temperature to the observed trends, which 

would minimize both false-positive and false-negative decisions about aquatic life use support.

UT DEQ uses a mathematical model, River Invertebrate Prediction and Classification System (RIVPACS), 

to predict the expected composition of benthic macroinvertebrate species inhabiting streams from 

observations made at numerous streams that are relatively unimpacted by anthropogenic stress. The 

expected composition provides the baseline against which a test stream is compared. The results of the 

study show that changes in climate-related parameters used as predictor variables in the model will 

potentially alter the model’s precision. The model needs to be calibrated for the climate-sensitive 

parameters so that effects from global climate change (regardless of whether they are natural or 

enhanced by anthropogenic sources of carbon to the atmosphere) and effects from anthropogenic 

stress (e.g., toxic discharges, stormwater flows, nutrient enrichment) can be distinguished. UT DEQ 

recalibrates the model every 2 years for Integrated Report purposes. Recalibration includes new 

reference sites, updated data from existing reference sites, and new environmental predictor variables 

and data. Therefore, as part of its existing program, Utah is able to accommodate and adjust for changes 

to predictor variables due to climate change, provided that it is aware of the potential for systematic 

bias.

To continue support of the effort, UT DEQ intends to collect additional data at long-term reference sites. 

Using the initial 2006 RIVPACS model as baseline, which includes most historical data from reference 

sites, at least five sites from each of the eight biologically similar groups will be sampled. A site will be 

sampled when the basin rotation monitoring plan is implemented for that basin (six-basin rotation). The 

sites encompass various levels of elevation, watershed size, latitude, and such, which can provide clues 

where climate-change effects are most pronounced. The RIVPACS model will be recalibrated every 

2 years including new reference sites and updated predictor variable data. These recalibrated models 

will then be applied to data collected from the revisited trend reference sites to quantify several 

measures of long-term biological changes, including observed/expected (O/E) trends sites, changes in 

biological group membership, and taxon-level changes within group membership, including patterns in 

trait-based community composition. Site-specific results from these recalibrated models will also be 

compared to historical results to evaluate the extent to which climate trends would have altered 

decisions regarding support or non-support of aquatic life uses if climate-related biases were not 

accounted for in the analyses.
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3.16 Applications of Biological Assessment at Multiple Scales in Coral Reef, 

Estuarine, and Coastal Programs

Background 

Biological assessments can be conducted at many spatial scales and at many levels of biological 

organization. Spatial scale refers to the area considered in a biological assessment and can range from a 

shoreline or stream reach to an entire waterbody, region, state, or nation. Level of biological 

organization makes note that biology self-organizes into levels of order or structure such as organism, 

population, community, biotope, bioregion, or biome. Each level is generally associated with a physical 

space, such as habitat, landscape, watershed, or region. For example, biological assessment is a valuable 

tool to examine a single stream reach by considering the biological community within a defined habitat 

or a consolidated group of habitats in the stream (USEPA 1990, 1999). Such habitat-specific communitylevel biological assessments can also be conducted at local, state, and national spatial scales. U.S. 

Environmental Protection Agency’s (EPA’s) National Coastal Assessments (2001–2006) and National 

Coastal Condition Assessment (2010)18—programs designed to assess the condition of the nation’s

estuaries and coastal waters—conduct habitat-specific community-level biological assessments 

(hereafter referred to as habitat-level assessments) at the national scale. Habitat-level assessments are 

consistent with the definition of biological integrity as the capability of supporting and maintaining a 

balanced, integrated, adaptive community of organisms having a composition and diversity comparable 

to those of natural habitats of the region (Frey 1975; modified by Karr and Dudley 1981).

At a different level of biological organization, several methods for biological assessment that are specific 

to the aquatic landscape or to landscape-level processes have been developed. These methods can be 

useful tools in spatially complex waterbodies that are defined by interconnections among biological 

communities and among many distinct environments or habitats. Landscape-level concepts can be 

applied to all waterbody types and provide particular insights for watershed management. They are 

potentially very helpful as evaluative tools in waterbodies that appear as intertwined, patchy (and often 

shifting) mosaics of environments that support different biota and respond differently to different 

stressors. 

 

18 For more information, see http://water.epa.gov/type/oceb/assessmonitor/nccr/index.cfm. 

Abstract

Biological assessments provide useful information on the cumulative impacts of multiple 

stressors on biological conditions. As integrators, biological assessments can also evaluate 

the effects of landscape and ecological processes on aquatic life. By applying biological 

assessments at multiple spatial scales and multiple levels of biological organization in large 

and spatially complex waterbodies such as estuaries, coral reefs, or large braided river 

networks, U.S. Environmental Protection Agency hopes to expand its ability to understand 

first the interactions of biological communities with the large-scale processes that define 

ecosystems and second the cumulative effects of multiple stressors over larger spatial scales 

and over decadal time periods. Approaches combining biological assessments at several 

scales and levels are being developed for estuaries in the National Estuary Program and for 

coral reefs.
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Coral Reef Biological Assessments

The concept of biological integrity at the landscape level has, for example, been identified as important 

in developing biological criteria for coral reefs. Coral reefs are spatially complex habitats that are 

inextricably intertwined with a larger set of adjacent habitats (e.g., mangroves and seagrasses). Coral 

reef biota have evolved life history strategies that rely on the availability of those adjacent habitats

(Christensen et al. 2003; Mumby et al. 2004, 2008; Aguilar-Perera and Appeldoorn 2007; McField and

Kramer 2007; Meynecke et al. 2008; Sale et al. 2008). EPA’s Coral Reef Biological Criteria document 

(Bradley et al. 2010) points out that “[b]iological integrity also means that reef organisms...have a clean, 

healthy environment to support them, including habitats for propagation, nurseries, and refugia. In this 

context, a fully functioning coral reef ecosystem may include adjacent supporting ecosystems such as 

seagrasses and mangroves.” That document also recommends area measures of coral reef extent 

(e.g., square meters) as a first-order method for biological assessment of coral reefs that is relevant to 

landscape-scale evaluations. While most monitoring programs portray coral quantity as twodimensional (2-D) live coral cover, EPA has developed a rapid survey procedure for estimating threedimensional (3-D) total coral cover, which more realistically characterizes coral structure available as 

community habitat (Fisher 2007; Fisher, Davis, et al. 2007; Fisher, Fore, et al. 2008).

In conjunction with National Oceanic and Atmospheric Administration (NOAA) and other partners, 

scientists from EPA’s Atlantic and Gulf Ecology Divisions (Narragansett and Gulf Breeze) are exploring 

the use of biological assessments to describe the coral reef and fish community along a gradient of 

stress in Guánica Bay, Puerto Rico. This effort may expand to include other critical coastal habitats in the 

future, e.g., sea grass beds and mangrove forests. Scientists will examine the pollution sensitivity of 

different taxa, presence or absence of native species, and other ecological response variables and then 

map the changes in these variables along a gradient of increasing stress—a Biological Condition Gradient

(BCG) (see Chapter 2, Tool #2). Additionally, if there is sufficient quality and quantity of field data 

available, the BCG can provide a framework for relating well documented numeric stressor-response 

relationships to biological condition and thereby more precisely define stressor concentrations that 

support a waterbody’s designated aquatic life use. Establishing this relationship could involve two steps.

One step is establishing a numeric biological threshold that corresponds to the desired level of biological 

condition. For example, State and Tribal programs often develop numeric biological thresholds based on 

reference site conditions using an index of biotic integrity (IBI) or modeling the ratio of observed to 

expected species (O/E). Quantifying the relationship between BCG tier assignments and IBI or O/E scores 

for sampling sites along a gradient of stress provides a mechanism to link the scores to different levels of 

biological condition. The other step is quantifying the relationship between the IBI or O/E values and the 

stressor/parameter of interest such as nitrogen or phosphorus. Once a significant relationship between 

the IBI or O/E values and the stressor is documented, numeric water quality criteria (NWQC) for 

nitrogen or phosphorous could potentially be derived by selecting the stressor value that corresponds to 

the selected biological threshold (USEPA 2010a). This process facilitates the development of NWQC for 

nitrogen or phosphorus that are explicitly associated with levels of biological condition supportive of 

designated aquatic life uses. Developing these relationships at multiple scales including landscape-scale 

biological assessments will facilitate linking state and tribal water quality standards with both watershed 

and national estuary programs (Cicchetti and Greening 2011, USEPA In draft). 

Biological Assessment at Multiple Scales in Estuaries and Coastal Waters

A large body of estuarine work has been done in index development and in application of habitat-level 

biological assessments. For example, approaches have been developed for salt marshes, soft-bottom 

benthic invertebrate communities and seagrass beds (USEPA 2000b). As a supplement to these efforts, 
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October 2011 69

several environmental programs such as EPA’s national estuary programs (NEPs) are working together 

with U.S. Environmental Protection Agency (EPA) Office of Research and Development to develop 

landscape-scale biological assessment tools to evaluate and understand large-scale changes that have 

occurred to multiple habitats over long time periods and to integrate them into management in 

conjunction with existing habitat-level biological assessment tools. Specifically, the Tampa Bay, 

Narragansett Bay, and Mobile Bay Estuary programs are evaluating complementary application of the 

BCG to estuaries at the individual habitat level of biological assessment and at the landscape level of 

biological assessment, for managing estuaries and watersheds at the spatial scale of the entire 

waterbody.

As an example of landscape level assessment, one method in development considers the habitat

landscape or biotope mosaic. A biotope is an area that is relatively uniform in physical structure and is 

identified by a dominant biota (Madden et al. 2009; Davies et al. 2004). Biotopes in estuaries include 

seagrass beds, salt marshes, coral reefs, clam flats, and more. Biotopes are a foundation of many recent 

habitat classification schemes, including the Coastal and Marine Ecological Classification Standard, which 

has been sponsored by the Federal Geographic Data Committee, and the European Nature Information 

System (Davies et al. 2004). Arrangements of biotopes provide species with spawning grounds, 

nurseries, refuge, sustenance, and other vital needs; such arrangements are particularly critical for 

larger mobile species and for species that move among biotopes at different stages of their life. The 

areas and arrangements of biotopes in a waterbody are affected by the full range of anthropogenic 

stressors, including nitrogen and phosphorus pollution, toxics, shoreline development, and sediment 

loads. Because biotopes are inherently a biological component, NEPs are developing approaches for 

biological assessment that consider areas and distributions of biotopes and biotope landscapes at the 

whole-estuary scale, combining the landscape-level tools with more resolved habitat-level tools. Tampa 

Bay, Narragansett Bay, and other NEPs are working on these multi-level BCG approaches. Additionally, 

the Mobile Bay NEP is exploring how to incorporate the concept of ecosystem services in development 

of a Biological Condition Gradient for the estuary. Current efforts in Tampa Bay and Narragansett Bay 

are briefly discussed below.

Tampa Bay Estuary Program

The Tampa Bay Estuary Program (TBEP) initiated a system-wide management framework in the 1990s

that developed estuarine habitat restoration and protection goals to support estuarine-dependent 

Definitions:

• Habitat-level biological assessments—Evaluations of biological condition that consider 

biological communities within a defined habitat or suite of habitats (see Frey 1975; Karr 

and Dudley 1981).

• Landscape-level biological assessments—Evaluations of biological condition that consider 

and attempt to integrate biological processes, multiple biological habitats, or multiple 

biological communities within a defined landscape, waterbody, watershed, or waterbody 

type. The extent or arrangement (or both) of multiple biological habitats in a defined 

waterbody type. 

 Both of these types of assessments can apply at a wide range of spatial scales, from a 

single area or subembayment to a larger waterbody, state, region, or nation. 
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October 2011 70

species and the habitat landscapes they require (e.g., the extent of seagrass beds, mangrove forests, 

Spartina marshes, Salicornia marshes, and low-salinity marshes). Although the term biotope was not 

used, the framework employed the basic concepts of biotope extent and distribution to evaluate 

condition of the waterbody, comparing current condition to a more naturally occurring condition that 

existed at a relatively undisturbed point in the past. This information supported the development of 

environmental protection and restoration goals for the waterbody and watershed that move the estuary 

closer to those more naturally occurring conditions. This approach was combined with habitat-level 

work, including water quality modeling to predict seagrass health, benthic macroinvertebrate surveys, 

and more. Tampa Bay has recovered many hundreds of acres of high-value biotopes (Cloern 2001; 

Duarte 2009). TBEP is now working with other NEPs to develop those approaches into transferable 

biological assessment tools using concepts from the BCG. The methods used by TBEP, together with 

their application to biological assessment at landscape scales, are discussed in Cicchetti and Greening 

(2011). 

Narragansett Bay Estuary Program

The Narragansett Bay Estuary Program (NBEP) and partners, benefiting from the Tampa Bay experience, 

are developing a suite of biological assessment tools to apply on a range of biological levels and spatial 

scales. A pilot program in Greenwich Bay, a sub-estuary of Narragansett Bay, has examined 

macroinvertebrate communities and biotopes in the context of the BCG using historical documentation 

of early stressor levels and ecosystem conditions to recreate a biological baseline. The project is 

especially pertinent to highly altered systems where it is often impossible to find undisturbed or 

minimally disturbed conditions. To characterize the biological responses to increasing stress, the study 

identified current, recent and historical stressors to Greenwich Bay benthos, including water quality 

(e.g., hypoxia), sediment metals, nutrients (i.e., nitrogen-loading), and hydrodynamics (including 

dredging and shoreline modification), terrestrial runoff, storms, and temperature. Changes in these 

parameters through time were summarized. A critical but challenging aspect of the project was to 

establish a reference level, or minimally disturbed endpoint. Target reference levels derived from 

historical baselines can be problematic because (1) they are difficult to calibrate with current ecosystem 

status, (2) ecosystems were as dynamic in the past as they are today, and (3) climate change and the 

degree of anthropogenic influence can render these endpoints unattainable. However, Greenwich Bay is 

fortunate in having available a significant amount of cultural and scientific historical data; although 

much of the information is qualitative, even qualitative differences in the biological indicators can be 

useful for defining a minimally disturbed endpoint. Ecological timeline data were overlaid with a 

detailed cultural timeline in order to associate changes in biological indicators with changes in human 

activities. Records of significant storms and climate trends gave broader context to ecological 

observations. The combined cultural and ecological timeline suggest when thresholds in the biological 

indicators may have been exceeded.

Because nutrient pollution is a major stressor in Narragansett Bay, the tools consider habitats and 

landscapes that are sensitive to (and diagnostic of) nutrient stress. At the habitat scale, NBEP and EPA’s 

Atlantic Ecology Division (Narragansett) are developing approaches for biological assessment of 

macroinvertebrates in deeper subtidal areas, camera-based approaches to examine biology in deeper 

subtidal areas, and approaches for evaluating seagrass and microalgae as tools to better manage 

nutrient inputs to the waterbody and watershed. The overall project goal is to develop an estuarine 

framework that can apply at multiple scales and levels using several methods of biological assessment, 

all brought together with the “common language” of the BCG.
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October 2011 71

Transferability to Freshwater Aquatic Ecosystems

By performing biological assessments and developing BCGs at multiple spatial scales and levels of 

biological organization in estuaries and coral reef ecosystems, EPA, NOAA, and their NEP partners will 

better understand the interactions among biological communities with system-level processes that 

define and regulate ecosystems, and will be able to assess the cumulative effects of multiple stressors 

over large spatial scales and over longer periods of time (e.g., decadal). The results of this work are

expected to be adapted to large and complex freshwater systems, such as braided river networks, lakes, 

and large rivers and their attendant watersheds. In river systems, for example, EPA’s Ecological Exposure 

Research Division (Cincinnati) is developing geographic information system- (GIS-) based tools to classify 

and characterize natural variability in watersheds and concurrently developing watershed-scale models 

integrating habitat and landscape biological assessments of classified river systems, incorporating main 

channel and lateral slackwaters (bays, side channels, and backwaters) with the floodscape (isolated 

oxbows, lakes, wetlands, and usually dry alluvial floodplains). A major component of this work focuses

on defining critical ecological thresholds, or tipping points, of ecological condition and function in river 

systems in response to multiple stressors in watersheds at multiple spatial and temporal scales. 

Tools such as these could support watershed and basin wide management and planning, enabling state, 

tribal and local resource managers to: 1) account for more of the natural variability within and across 

river systems, watershed and regions; 2) relate changes in stressors exposure to changes in biological 

(and functional) condition at both a watershed and system-wide level; and, 3) facilitate the 

extrapolation of findings from one system and/or watershed to other similarly located or functioning

systems. 
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3.17 Partnerships in the Protection of Oregon’s Coho Salmon

Introduction 

For more than a decade, state and federal agencies have been working to halt the decline of coho 

salmon in Oregon. In 1997 Oregon implemented the Oregon Plan for Salmon and Watersheds, a step 

toward reversing the decline of coho salmon in Oregon coastal streams. In response, Oregon 

Department of Environmental Quality (ODEQ) and Oregon Department of Fish and Wildlife (ODFW) 

began expanded monitoring in Oregon coastal streams to gather information on the status of water 

quality and watershed health indicators identified as potential causes for declining populations of 

Oregon coastal coho salmon (State of Oregon 1997).

In 2005 ODEQ and ODFW assessed the information collected on the factors for the decline of coho and 

evaluated the relative importance of each factor to the continued viability of Oregon’s coastal coho runs 

into the future. Specifically, ODEQ and ODFW assessed data for the Oregon Coast Coho Evolutionarily 

Significant Unit (ESU). The Oregon Coast Coho ESU is in western Oregon, spanning approximately threequarters of the coastline with the Pacific Ocean and contains more than 9,000 miles of rivers and 

streams. Most of the stream miles (more than 80 percent) are small, wadeable streams (1st through 3rd

order). Two hundred and eighty-three randomly selected sites were characterized throughout the ESU, 

ranging from 61 to 86 sites per monitoring area. Specifically, data were analyzed for four monitoring 

areas nested within the ESU (North Coast, Mid-Coast, Mid-South Coast, and Umpqua).

In 2007 ODFW released the final draft of the Oregon Coast Coho Conservation Plan (State of Oregon 

2007), which outlines Oregon’s strategy to ensure the continued viability of threatened coastal coho 

salmon runs. Part of the plan identifies the need for higher-resolution monitoring of water quality and 

macroinvertebrates in the Oregon Coast Coho ESU (Lawson et al. 2007). Because of the ability of 

macroinvertebrates to integrate the effects of water quality and habitat stressors—and limited 

resources for comprehensive monitoring—ODEQ and ODFW agreed that macroinvertebrates would be 

used to relate water quality and overall watershed condition in the ESU. In 2008, National Oceanic and 

Atmospheric Administration (NOAA) Fisheries Division used the information in its final decision to re-list 

Oregon coastal coho as threatened under the Endangered Species Act.

Abstract

Assessment of biological conditions in Oregon’s Coast Coho Evolutionarily Significant Unit 

(ESU) has provided state agencies with valuable information that can be used to improve 

protection of coho salmon. Oregon Department of Environmental Quality and Oregon 

Department of Fish and Wildlife are using monitoring data to examine several indicators—

temperature and fine sediments—that have been identified as potential causes of coho 

population decline in the state. Findings show that the two monitoring areas with the 

highest biological condition also showed the lowest evidence of stress from temperature 

and fine sediment. National Oceanic and Atmospheric Administration’s Fisheries Division 

has also been able to use biological information to support a decision to list coho as 

threatened and to designate the Oregon Coast Coho ESU as a critical habitat.
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October 2011 73 

Assessment of Biological Condition

In 2006–2007 ODEQ and ODFW jointly collected and analyzed macroinvertebrate data in the ESU. They 

evaluated biological condition for each of four monitoring areas in the ESU. Macroinvertebrates were 

also used as a screening tool to determine the relative contributions of temperature and fine sediment 

as stressors to biological condition.

A multivariate predictive model, PREDATOR, was used to assess the biological condition of wadeable 

streams throughout Oregon (Hubler 2008). The model compares observed taxa with expected taxa to 

generate an observed/expected (O/E) taxa ratio. Scores of less than 1.0 have fewer taxa at a site than 

were predicted by the model, representing a loss of native reference taxa richness. Benchmarks based 

on the distribution of O/E scores at reference sites were used to classify the samples into one of the

three following biological condition classes: least disturbed, moderately disturbed, and most disturbed

(Table 3-12).

Table 3-12. Biological benchmarks. 

Biological condition class O/E Taxa loss

Least disturbed > 0.91 8% or less

Moderately disturbed 0.86–0.91 9%–14%

Most disturbed < 0.86 15% or more

Subsequent monitoring showed that approximately 50 percent of the streams could be classified as 

least disturbed (equivalent to reference), while almost 40 percent of streams in the ESU had 

macroinvertebrates in most disturbed conditions (missing a considerable amount of reference taxa). The 

four monitoring units showed different relative proportions of condition classes. The Mid-Coast 

monitoring area had the largest proportion of sites in highest biological condition with 69 percent of 

sites in least disturbed condition and 17 percent of sites in most disturbed condition. The Umpqua 

monitoring unit showed only about one-quarter of sites in least disturbed conditions and approximately 

two-thirds of sites in most disturbed conditions. That information, along with stressor information for 

each monitoring unit, became very important in developing the stressor-response model. The 

information was used to try to identify the relative importance of two key (NPS) stressors to 

macroinvertebrate conditions in the Oregon Coastal Coho ESU.

Stressor-Response Model 

The relationships among macroinvertebrate abundances and environmental variables (seasonal 

maximum temperature and percent fines) were used to model the optimum conditions for each taxon.

These optimal conditions were then used to infer the overall assemblage preference for temperature 

and fine sediments of any site using a macroinvertebrate sample alone (Huff et al. 2006). Benchmarks 

were established to identify sites where temperature or fine sediments or both can be at levels 

considered to be stressful to the macroinvertebrate assemblages. Temperature stress (TS) values above 

18 °C were considered temperature stressed, as it relates directly to the WQS set to protect salmon and 

trout rearing and migration. Fine sediment stress (FSS) values above 10 percent were considered 

sediment stressed because that value has been shown to negatively affect macroinvertebrates in 

mountain streams (Bryce et al. 2010).
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October 2011 74

The North Coast monitoring area showed the lowest levels of TS (36 percent of sites) and FSS 

(22 percent). The Mid-Coast monitoring area showed approximately half of the sites as stressed for both 

temperature and fine sediment, despite showing the highest percentage of sites in least disturbed 

biological condition. Both the Mid-South and Umpqua monitoring areas showed two-thirds or more of 

the sites to be stressed for both temperature and fine sediment. Apart from the North Coast, stresses to 

the macroinvertebrate assemblages from temperature and fine sediments appear to be equivalent.

Conclusions 

Biological data and stressor-response relationships were used as the basis for several findings. First,

NOAA was able to make a decision to list coho as threatened and to designate the Oregon Coast ESU as 

a critical habitat. Second, several general trends were observed in the assessment of the 

macroinvertebrate data collected and assessed. The two monitoring areas with the highest biological 

condition (North Coast and Mid-Coast) showed the lowest evidence of stress from temperature and fine 

sediment. The Mid-South Coast and Umpqua monitoring areas showed higher levels of stress and lower 

biological condition (substantially so in the Umpqua). That information can be used in developing 

management plans for ESU monitoring areas or basins. Much emphasis has been placed on improving 

the temperature conditions in Oregon’s streams and rivers, while less work has gone into developing 

sediment management plans. The data presented here suggest that excess fine sediments are affecting 

biological conditions in the ESU on a scale similar to that of temperature.

Finally, the monitoring project is an example of two state agencies working together to implement a 

monitoring program that is cost-effective by addressing both agencies’ needs for information. For 

ODFW, the random macroinvertebrate, water quality, and habitat sampling protocol provides critical 

information on water quality and habitat conditions, which have been identified as limiting factors to 

coho salmon viability. For ODEQ, the macroinvertebrate sampling in conjunction with the water quality 

and habitat monitoring provides valuable information on attainment of the designated aquatic life uses 

for streams.
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October 2011 75

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<http://www.epa.gov/npdes/pubs/owm0264.pdf>. Accessed September 2011.

USEPA (U.S. Environmental Protection Agency). 1991b. Policy on the Use of Biological Assessments and 

Criteria in the Water Quality Program. U.S. Environmental Protection Agency, Washington, DC.

<http://www.epa.gov/bioiweb1/pdf/PolicyonBiologicalAssessmentsandCriteria.pdf>. Accessed 

September 2011.

USEPA (U.S. Environmental Protection Agency). 1994. Water Quality Standards Handbook. 2nd ed. EPA823-B-94-005. U.S. Environmental Protection Agency, Washington, DC. 

<http://water.epa.gov/scitech/swguidance/waterquality/standards/handbook/index.cfm>. 

Accessed September 2011. 

USEPA (U.S. Environmental Protection Agency). 1999. Rapid Bioassessment Protocols for Use in Streams 

and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish. 2nd ed. EPA 841-B-99-

002. U.S. Environmental Protection Agency, Office of Water, Washington, DC. 

<http://water.epa.gov/scitech/monitoring/rsl/bioassessment/index.cfm>. Accessed September 

2011. 

USEPA (U.S. Environmental Protection Agency). 2000a. Stressor Identification Guidance Document. EPA822-B-00-025. U.S. Environmental Protection Agency, Washington, DC. 

<http://www.epa.gov/waterscience/biocriteria/stressors/stressorid.pdf>. Accessed September 

2011. 

USEPA (U.S. Environmental Protection Agency). 2000b. Estuarine and Coastal Marine Waters: 

Bioassessment and Biocriteria Technical Guidance. EPA 822-B-00-024. U.S. Environmental 

Protection Agency, Office of Water, Washington, DC. 

<http://water.epa.gov/scitech/swguidance/waterquality/standards/criteria/aqlife/biocriteria/

upload/2009_04_22_biocriteria_States_estuaries_estuaries-2.pdf>. Accessed September 2011. 

USEPA (U.S. Environmental Protection Agency). 2002. Summary of Biological Assessment Programs and 

Biological Criteria Development for States, Tribes, Territories and Interstate Commissions: Streams 

and Wadeable Rivers. EPA-822-R-02-048. U.S. Environmental Protection Agency, Office of Water, 

Washington, DC. <http://www.epa.gov/bioiweb1/html/program_summary.html>. Accessed 

September 2011.

USEPA (U.S. Environmental Protection Agency). 2003. Elements of a State Water Monitoring and 

Assessment Program. EPA 841-B-03-003. U.S. Environmental Protection Agency, Washington, DC. 

<http://water.epa.gov/type/watersheds/monitoring/index.cfm>. Accessed September 2011.

USEPA (U.S. Environmental Protection Agency). 2006. Wadeable Streams Assessment. EPA 841-B-06-

002. U.S. Environmental Protection Agency, Office of Research and Development and Office of 

Water, Washington, DC. <http://water.epa.gov/type/rsl/monitoring/streamsurvey/index.cfm>. 

Accessed September 2011. 
A Primer on Using Biological Assessments to Support Water Quality Management

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USEPA (U.S. Environmental Protection Agency). 2007. Watershed-based National Pollutant Discharge 

Elimination System (NPDES) Permitting Technical Guidance. EPA 833-B-07-004. U.S. Environmental 

Protection Agency, Office of Wastewater Management, Washington, DC. 

<http://www.epa.gov/npdes/pubs/watershed_techguidance.pdf>. Accessed September 2011. 

USEPA (U.S. Environmental Protection Agency). 2010a. Using Stressor-response Relationships to Derive 

Numeric Nutrient Criteria. EPA-820-2-10-001. U.S. Environmental Protection Agency. 

<http://water.epa.gov/scitech/swguidance/standards/criteria/nutrients/upload/finalstressor2010

.pdf>. Accessed September 2011.

USEPA (U.S. Environmental Protection Agency). 2010b. Causal Analysis/Diagnosis Decision Information 

System (CADDIS). Office of Research and Development, Washington, DC. 

<http://www.epa.gov/caddis>. Website last updated September 23, 2010. Accessed September 

2011. 

USEPA (U.S. Environmental Protection Agency). 2010c. Implications of Climate Change for State 

Bioasssessment Programs and Approaches to Account for Effects (External Review Draft). U.S. 

Environmental Protection Agency, Office of Research and Development, Washington, DC.

<http://cfpub.epa.gov/ncea/global/recordisplay.cfm?deid=233810>. Accessed September 2011.

USEPA (U.S. Environmental Protection Agency). 2012. Recovery Potential Screening. U.S. Environmental 

Protection Agency, Office of Wetlands, Oceans and Watersheds. Washington, DC. 

<http://www.epa.gov/recoverypotential/> Accessed January 2012.

USEPA (U.S. Environmental Protection Agency). In draft. Identifying and Protecting Healthy Watersheds: 

A Technical Guide (Draft). U.S. Environmental Protection Agency, Office of Wetlands, Oceans, and 

Watersheds. Washington, DC. <http://water.epa.gov/polwaste/nps/watershed/index.cfm>. In 

process of finalization. Release expected 2012.

Walter, R.C., and D.J. Merritts. 2008. Natural streams and the legacy of water-powered mills. Science

319:299–304. 

Yoder C.O., and J.E. DeShon. 2003. Using biological response signatures in a framework of multiple 

indicators to assess and diagnose causes and sources of impairments to aquatic assemblages in 

selected Ohio rivers and streams. In Biological Response Signatures: Indicator Patterns using 

Aquatic Communities, ed. T.P. Simon, pp. 23–81. CRC Press, Boca Raton, FL. 

Yoder, C.O., and E.T. Rankin. 1995. Biological Response Signatures and the Area of Degradation Value: 

New Tools for Interpreting Multimetric Data. In Biological Assessment and Criteria: Tools for 

Water Resource Planning and Decision Making, ed. W.S. Davis and P. Simon, pp. 263–286. Lewis 

Publishers, Boca Raton, FL. 
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 81

Glossary 

aquatic assemblage An association of interacting populations of organisms in a 

given waterbody; for example, fish assemblage or a benthic 

macroinvertebrate assemblage. 

aquatic community An association of interacting assemblages in a waterbody, the 

biotic component of an ecosystem. 

aquatic life use A beneficial use designation in which the waterbody provides,

for example, suitable habitat for survival and reproduction of 

desirable fish, shellfish, and other aquatic organisms. 

attribute The measurable part or process of a biological system.

benthic macroinvertebrates or 

benthos

Animals without backbones, living in or on the sediments, of a 

size large enough to be seen by the unaided eye and which can 

be retained by a U.S. Standard no. 30 sieve (28 meshes per 

inch, 0.595-mm openings); also referred to as benthos, infauna, 

or macrobenthos. 

best management practice An engineered structure or management activity, or 

combination of those, that eliminates or reduces an adverse 

environmental effect of a pollutant. 

biological assessment or 

bioassessment

An evaluation of the biological condition of a waterbody using 

surveys of the structure and function of a community of 

resident biota. 

biological criteria or biocriteria Narrative expressions or numeric values of the biological 

characteristics of aquatic communities based on appropriate 

reference conditions; as such, biological criteria serve as an 

index of aquatic community health. 

biological indicator or bioindicator An organism, species, assemblage, or community characteristic 

of a particular habitat, or indicative of a particular set of 

environmental conditions. 

biological integrity The ability of an aquatic ecosystem to support and maintain a 

balanced, adaptive community of organisms having a species 

composition, diversity, and functional organization comparable 

to that of natural habitats in a region. 

biological monitoring or 

biomonitoring

Use of a biological entity as a detector and its response as a 

measure to determine environmental conditions; ambient 

biological surveys and toxicity tests are common biological 

monitoring methods. 

biological survey or biosurvey Collecting, processing, and analyzing a representative portion 

of the resident aquatic community to determine its structural 

and/or functional characteristics. 
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biotope An area that is relatively uniform in physical structure and that 

is identified by a dominant biota. 

Clean Water Act The act passed by the U.S. Congress to control water pollution 

(formally referred to as the Federal Water Pollution Control Act 

of 1972). Public Law 92-500, as amended. 33 U.S.C. 1251 et seq. 

Clean Water Act 303(d) This section of the act requires states, territories, and 

authorized tribes to develop lists of impaired waters for which 

applicable WQS are not being met, even after point sources of 

pollution have installed the minimum required levels of 

pollution control technology. The law requires that the 

jurisdictions establish priority rankings for waters on the lists 

and develop TMDLs for the waters. States, territories, and 

authorized tribes are to submit their lists of waters on April 1 in 

every even-numbered year.

Clean Water Act 305(b) Biennial reporting requires description of the quality of the 

nation’s surface waters, evaluation of progress made in 

maintaining and restoring water quality, and description of the 

extent of remaining problems. 

criteria Elements of state water quality standards, expressed as 

constituent concentrations, levels, or narrative statements, 

representing a quality of water that supports a particular use. 

When criteria are met, water quality will generally protect the 

designated use.

designated uses Those uses specified in WQS for each waterbody or segment 

whether or not they are being attained. 

disturbance Human activity that alters the natural state and can occur at or 

across many spatial and temporal scales. 

ecological integrity The condition of an unimpaired ecosystem as measured by 

combined chemical, physical (including physical habitat), and 

biological attributes. Ecosystems have integrity when they have 

their native components (plants, animals and other organisms) 

and processes (such as growth and reproduction) intact.

ecoregion A relatively homogeneous ecological area defined by similarity 

of climate, landform, soil, potential natural vegetation, 

hydrology, or other ecologically relevant variables. 

function Processes required for normal performance of a biological 

system (may be applied to any level of biological organization). 

guild A group of organisms that exhibit similar habitat requirements 

and that respond in a similar way to changes in their 

environment. 
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historical data Data sets from previous studies, which can range from 

handwritten field notes to published journal articles. 

index of biological/biotic integrity An integrative expression of site condition across multiple 

metrics; an IBI is often composed of at least seven metrics. 

invasive species A species whose presence in the environment causes economic 

or environmental harm or harm to human health. Native 

species or nonnative species can show invasive traits, although 

that is rare for native species and relatively common for 

nonnative species. (Note that this term is not included in the 

biological condition gradient [BCG].) 

least disturbed condition The best available existing conditions with regard to physical, 

chemical, and biological characteristics or attributes of a 

waterbody within a class or region. Such waters have the least 

amount of human disturbance in comparison to others in the 

waterbody class, region, or basin. Least disturbed conditions 

can be readily found but can depart significantly from natural, 

undisturbed conditions or minimally disturbed conditions.

Least disturbed condition can change significantly over time as 

human disturbances change.

maintenance of populations Sustained population persistence; associated with locally 

successful reproduction and growth. 

metric A calculated term or enumeration that represents some aspect 

of biological assemblage, function, or other measurable aspect 

and is a characteristic of the biota that changes in some 

predictable way with increased human influence. 

minimally disturbed condition The physical, chemical, and biological conditions of a 

waterbody with very limited, or minimal, human disturbance. 

multimetric index An index that combines indicators, or metrics, into a single 

index value. Each metric is tested and calibrated to a scale and 

transformed into a unitless score before being aggregated into 

a multimetric index. Both the index and metrics are useful in 

assessing and diagnosing ecological condition. See index of 

biological/biotic integrity (IBI).

narrative biological criteria Written statements describing the structure and function of 

aquatic communities in a waterbody that support a designated 

aquatic life use. 

native An original or indigenous inhabitant of a region; naturally 

present. 
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nonnative or intentionally 

introduced species

With respect to an ecosystem, any species that is not found in 

that ecosystem; species introduced or spread from one region 

of the United States to another outside their normal range are 

nonnative or non-indigenous, as are species introduced from 

other continents.

numeric biological criteria Specific quantitative measures of the structure and function of 

aquatic communities in a waterbody necessary to protect a

designated aquatic life use. 

periphyton A broad organismal assemblage composed of attached algae, 

bacteria, their secretions, associated detritus, and various 

species of microinvertebrates. 

rapid bioassessment protocols Cost-effective techniques used to survey and evaluate the 

aquatic community to detect aquatic life impairments and their 

relative severity. 

reference condition (biological 

integrity)

The condition that approximates natural, unaffected conditions 

(biological, chemical, physical, and such) for a waterbody.

Reference condition (biological integrity) is best determined by 

collecting measurements at a number of sites in a similar 

waterbody class or region undisturbed by human activity, if 

they exist. Because undisturbed conditions can be difficult or 

impossible to find, minimally or least disturbed conditions, 

combined with historical information, models, or other 

methods can be used to approximate reference condition as 

long as the departure from natural or ideal is understood.

Reference condition is used as a benchmark to determine how 

much other waterbodies depart from this condition because of

human disturbance.

See definitions for minimally and least disturbed condition

reference site A site selected for comparison with sites being assessed. The 

type of site selected and the types of comparative measures 

used will vary with the purpose of the comparisons. For the 

purposes of assessing the ecological condition of sites, a 

reference site is a specific locality on a waterbody that is 

undisturbed or minimally disturbed and is representative of the 

expected ecological integrity of other localities on the same 

waterbody or nearby waterbodies. 

refugia Accessible microhabitats or regions in a stream reach or 

watershed where adequate conditions for organism survival 

are maintained during circumstances that threaten survival; for 

example, drought, flood, temperature extremes, increased 

chemical stressors, habitat disturbance. 
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sensitive taxa Taxa intolerant to a given anthropogenic stress; first species 

affected by the specific stressor to which they are sensitive and 

the last to recover following restoration. 

sensitive or regionally endemic 

taxa

Taxa with restricted, geographically isolated distribution 

patterns (occurring only in a locale as opposed to a region), 

often because of unique life history requirements. Can be longlived, late-maturing, low-fecundity, limited-mobility, or require 

mutualist relation with other species. Can be among listed 

endangered/threatened or special concern species.

Predictability of occurrence often low; therefore, requires 

documented observation. Recorded occurrence can be highly 

dependent on sample methods, site selection, and level of 

effort.

sensitive - rare taxa Taxa that naturally occur in low numbers relative to total 

population density but can make up large relative proportion of 

richness. Can be ubiquitous in occurrence or can be restricted 

to certain micro-habitats, but because of low density, recorded 

occurrence is dependent on sample effort. Often stenothermic 

(having a narrow range of thermal tolerance) or coldwater 

obligates; commonly k-strategists (populations maintained at a 

fairly constant level; slower development; longer life span). Can

have specialized food resource needs or feeding strategies. 

Generally intolerant to significant alteration of the physical or 

chemical environment; are often the first taxa observed to be 

lost from a community.

sensitive - ubiquitous taxa Taxa ordinarily common and abundant in natural communities 

when conventional sample methods are used. Often having a 

broader range of thermal tolerance than sensitive or rare taxa. 

These are taxa that constitute a substantial portion of natural 

communities and that often exhibit negative response (loss of 

population, richness) at mild pollution loads or habitat 

alteration.

stressors Physical, chemical, and biological factors that adversely affect 

aquatic organisms. 

structure Taxonomic and quantitative attributes of an assemblage or

community, including species richness and relative abundance 

structurally and functionally redundant attributes of the system 

and characteristics, qualities, or processes that are represented 

or performed by more than one entity in a biological system. 

taxa A grouping of organisms given a formal taxonomic name such 

as species, genus, family, and the like. 
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taxa of intermediate tolerance Taxa that compose a substantial portion of natural 

communities; can be r-strategists (early colonizers with rapid 

turnover times; boom/bust population characteristics). Can be 

eurythermal (having a broad thermal tolerance range). Can

have generalist or facultative feeding strategies enabling 

utilization of relatively more diversified food types. Readily 

collected with conventional sample methods. Can increase in 

number in waters with moderately increased organic resources 

and reduced competition but are intolerant of excessive 

pollution loads or habitat alteration.

tolerant taxa Taxa that compose a small proportion of natural communities. 

They are often tolerant of a broader range of environmental 

conditions and are thus resistant to a variety of pollution- or 

habitat-induced stresses. They can increase in number 

(sometimes greatly) in the absence of competition. Commonly 

r-strategists (early colonizers with rapid turnover times; 

boom/bust population characteristics), able to capitalize when 

stress conditions occur; last survivors.

total maximum daily load The sum of the allowable loads of a single pollutant from all 

contributing point and nonpoint sources; the calculated

maximum amount of a pollutant a waterbody can receive and 

still meet WQS and an allocation of that amount to the 

pollutant’s source. 

toxicity identification evaluation A set of procedures to identify the specific chemicals 

responsible for effluent toxicity. 

toxicity reduction evaluation A site-specific study conducted in a stepwise process designed 

to identify the causative agents of effluent toxicity, isolate the 

sources of toxicity, evaluate the effectiveness of toxicity control 

options, and then confirm the reduction in effluent toxicity. 

water quality management 

(nonregulatory)

Decisions on management activities relevant to a water 

resource, such as problem identification, need for and 

placement of best management practices, pollution abatement 

actions, and effectiveness of program activity. 

water quality standard A law or regulation that consists of the designated use or uses 

of a waterbody, the narrative or numerical water quality 

criteria (including biological criteria) that are necessary to 

protect the use or uses of that waterbody, and an 

antidegradation policy. 
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whole effluent toxicity The aggregate toxic effect of an aqueous sample (e.g., whole 

effluent wastewater discharge) as measured by an organism's 

response after exposure to the sample (e.g., lethality, impaired 

growth or reproduction); WET tests replicate the total effect 

and actual environmental exposure of aquatic life to toxic 

pollutants in an effluent without requiring the identification of 

the specific pollutants. 
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Abbreviations and Acronyms

ADEQ Arizona Department of Environmental Quality

BCG biological condition gradient

BMIBI benthic macroinvertebrate index of biotic integrity

BMP best management practice

CADDIS Causal Analysis/Diagnosis Decision Information System

CT DEP Connecticut Department of Environmental Protection

CWA Clean Water Act

CWH coldwater habitat

EPA U.S. Environmental Protection Agency

EPT ephemeroptera, plecoptera, trichoptera taxa

ESU evolutionarily significant unit

EV exceptional value (Pennsylvania)

EWH exceptional warmwater habitat

FIBI fish index of biotic integrity

FQI Floristic Quality Index

FSS fine sediment stress

GIS geographic information system 

GPS global positioning system

HQ high-quality (Pennsylvania)

HUC hydrologic unit code

IBI index of biological/biotic integrity

IC impervious cover

ICI invertebrate community index

IDNR Iowa Department of Natural Resources 

INSTAR Interactive Stream Assessment Resource

IRG Integrated Reporting Guidance

LRW limited resource water

LWH limited warmwater habitat

MDE Maryland Department of the Environment

MDEQ Michigan Department of Environmental Quality

MDNR Maryland Department of Natural Resources

ME DEP Maine Department of Environmental Protection 

mIBI modified index of biological integrity

MIwb modified index of well-being

MPCA Minnesota Pollution Control Agency

MWH modified warmwater habitat

NARS National Aquatic Resource Surveys

NAWQA National Water-Quality Assessment

NBEP Narragansett Bay Estuary Program 
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NEP National Estuary Program

NFMR North Fork Maquoketa River 

NJ DEP New Jersey Department of Environmental Protection

NOAA National Oceanic and Atmospheric Administration

NPDES National Pollutant Discharge Elimination System

NPS nonpoint source

NTU nephelometric turbidity unit

NWQC numeric water quality criteria

O/E observed over expected

ODEQ Oregon Department of Environmental Quality

ODFW Oregon Department of Fish and Wildlife

ONRW Outstanding National Resource Water

ORD Office of Research and Development (U.S. Environmental Protection Agency)

PA DEP Pennsylvania Department of Environmental Protection

PREDATOR PREDictive Assessment Tool for Oregon

QHEI qualitative habitat evaluation index

RIVPACS River Invertebrate Prediction and Classification System 

SI stressor identification

SSH seasonal salmonid habitat

TBEP Tampa Bay Estuary Program

TIE toxicity identification evaluation 

TMDL Total Maximum Daily Load

TRE toxicity reduction evaluation

TS temperature stress

UAA use attainability analysis

UCONN University of Connecticut

USGS U.S. Geological Survey

UT DEQ Utah Department of Environmental Quality

VA DCR Virginia Department of Conservation and Recreation

VSA Virtual Stream Assessment

VT DEC Vermont Department of Environmental Conservation

WET whole effluent toxicity

WQL water quality limited

WQS water quality standards

WWH warmwater habitat

WWTF wastewater treatment facility

WWTP wastewater treatment plant
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Appendix A. Additional Resources

Biological Assessment and Biological Criteria: Technical Guidance

Biological assessment and biological criteria Description/summary

Biological Criteria: National Program for Surface Waters

(EPA 440-5-90-004) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1990

This document provides EPA regions, states and others with 

the conceptual framework and assistance necessary to 

develop and implement narrative and numeric biological 

criteria and to promote national consistency in application.

http://www.epa.gov/bioindicators/pdf/EPA-440-5-90-004Biologicalcriterianationalprogramguidanceforsurfacewaters.pdf

Policy on the Use of Bioassessments and Criteria in the Water 

Quality Program

Source: U.S. Environmental Protection Agency

Date of Publication: 1991

This document provides policy guidance on integration of

biological surveys, assessments, and criteria with chemicalspecific analysis and whole effluent and ambient toxicity 

testing methods in the water quality program.

http://www.epa.gov/bioiweb1/pdf/PolicyonBiologicalAssessmentsandCriteria.pdf

Coral reefs Description/summary

Stony Coral Rapid Bioassessment Protocol

(EPA 600-R-06-167) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2007

The principal purpose of the Stony Coral Rapid Bioassessment 

Protocol is to introduce a simple and rapid coral survey 

method that provides multiple biological indicators to 

characterize coral condition. The document offers insight on 

indicator relevance to ecosystem services (societal values), 

reef condition, and sustainability. It provides information 

regarding regulatory programs, and it presents a few 

examples describing how biological assessment indicators 

can be incorporated into a regulatory biological criteria

program to conserve coral resources.

http://www.epa.gov/bioindicators/pdf/EPA-600-R-06-167StonyCoralRBP.pdf

Coral Reef Biological Criteria: Using the Clean Water Act to 

Protect a National Treasure

(EPA-600-R-10-054) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2010 

Coral reef resource managers can use this document as a 

guide for developing and implementing biological criteria as 

part of water quality standards. Biological criteria are 

complementary to chemical and physical criteria and, once 

established, carry the same regulatory authority. The 

document introduces the role of biological criteria under the 

Clean Water Act and describes the process for identifying 

metrics, establishing reference values, designing a long-term 

monitoring program, and integrating biological criteria with 

existing management programs. It includes sections that link 

biological criteria to high-visibility issues such as ecosystem 

services, climate change, and ocean acidification.

http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=223392

Estuaries and coastal waters Description/summary

Estuarine and Coastal Marine Waters: Bioassessment and 

Biocriteria Technical Guidance

(EPA 822-B-00-024) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2000

This technical guidance provides an extensive collection of 

methods and protocols for conducting biological assessments 

in estuarine and coastal marine waters and the procedures 

for deriving biological criteria from the results.

See also National Coastal Condition Reports (2001, 2004 and 

2008) under National Aquatic Resource Surveys listed below.

http://www.epa.gov/waterscience/biocriteria/States/estuaries/estuaries.pdf
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Lakes and reservoirs Description/summary

Lakes and Reservoir Bioassessment and Biocriteria Technical 

Guidance Document

(EPA 841-B-98-007) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1998

This guidance is intended to provide managers and field 

biologists with functional methods and approaches that will 

facilitate the implementation of viable lake biological 

assessment and biological criteria programs that meet their 

needs and resources. Procedures for program design, 

reference condition determination, field biological surveys, 

biological criteria development, and data analysis are 

detailed. In addition, the document provides information on 

the application and effectiveness of lake biological 

assessment to existing EPA and state/tribal programs such as 

the Clean Lakes Program, 305(b) assessments, NPDES 

permitting, risk assessment, and watershed management.

See also National Lakes Assessment Report (2010) under

National Aquatic Resource Surveys listed below.

http://www.epa.gov/owow/monitoring/tech/lakes.html

Non-wadeable streams and rivers Description/summary

Concepts and Approaches for the Bioassessment of Nonwadeable Streams and Rivers

(EPA 600-R-06-127) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2006

This document provides a framework for the development of 

biological assessment programs and biological criteria for

large rivers. It helps states establish or refine their large river 

protocols for field sampling, laboratory sample processing, 

data management and analysis, and assessment and 

reporting.

http://www.epa.gov/eerd/rivers/non-wadeable_full_doc.pdf

Streams and wadeable rivers Description/summary

Biological Criteria: Technical Guidance for Streams and Small 

Rivers

(EPA 822-B-96-001) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2001

The goal of this document is to help states develop and use 

biological criteria for streams and small rivers. It includes a 

general strategy for biological criteria development, 

identifies steps in the process, and provides technical 

guidance on how to complete each step, using the 

experience and knowledge of existing state, regional, and 

national surface water programs.

See also Wadeable Streams Assessment Report (2006) under 

National Aquatic Resource Surveys listed below.

http://www.epa.gov/bioindicators/pdf/EPA-822-B-96-001BiologicalCriteria-TechnicalGuidanceforStreamsandSmallRiversrevisededition1996.pdf

Rapid Bioassessment Protocols for Use in Streams and 

Wadeable Rivers: Periphyton, Benthic Macroinvertebrates 

and Fish, 2nd ed.

(EPA 841-B-99-002) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1999

This document is a practical technical reference for 

conducting cost-effective biological assessments of lotic 

systems. The Rapid Bioassessment Protocols (RBPs) are a 

blend of existing methods used by various states to sample 

biological assemblages and assess physical habitat.

http://www.epa.gov/owow/monitoring/rbp/download.html
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Other Relevant Water Program Guidance

Listing and TMDLs Description/summary

Memorandum: Clarification of the Use of Biological Data and 

Information in the 2002 Integrated Water Quality Monitoring 

and Assessment Report Guidance

Source: U.S. Environmental Protection Agency

Date of Publication: 2002

This memorandum modified the 2002 Integrated Water 

Quality Monitoring and Assessment Report Guidance to 

provide clarity and promote consistency in the manner in 

which states use biological data and information in 

developing their submissions. 

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/biochange20302.cfm

Guidance for 1994 Section 303(d) Lists

Source: U.S. Environmental Protection Agency

Date of Publication: 1994

This memorandum clarified how biological data can be used 

to support listing of a waterbody on the section 303(d) list.

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/1994guid.cfm

Recovery Potential Screening

Source: U.S. Environmental Protection Agency

Date of Publication: 2012

The Recovery Potential Screening website is a user-driven, 

flexible approach for comparing relative differences in 

restorability among impaired waters. The screening process 

uses ecological, stressor, and social indicators to evaluate 

and compare waters and reveal factors that may explain the 

relative restorability of waters. This technical method and 

website are intended to assist in complex planning and 

prioritizing decisions, provide a systematic and transparent 

comparison approach, reveal underlying environmental and 

social factors that affect restorability, and better inform 

restoration strategies to help achieve results. The website 

provides step-by-step directions in the screening process, 

downloadable tools for calculating indices and displaying 

results, summaries of indicators and their measurement from 

common data sources, a recovery literature database, and 

several case studies and related links. 

http://www.epa.gov/recoverypotential/
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Monitoring and assessment Description/summary

Guidance for 2006 Assessment, Listing and Reporting

Requirements Pursuant to Sections 303(d), 305(b) and 314 of

the Clean Water Act

Source: U.S. Environmental Protection Agency

Date of Publication: 2005

This guidance is for states, territories, authorized tribes, and 

interstate commissions that help prepare and submit section 

305(b) reports (referred to as jurisdictions). It outlines the 

development of biennial Integrated Reports, which that 

would support EPA’s strategy for achieving a broad-scale, 

national inventory of water quality conditions.

The objective of this guidance is to provide jurisdictions (1) a 

recommended reporting format and (2) suggested content to 

be used in developing a single document that integrates the 

reporting requirements of CWA sections 303(d), 305(b), and 

314. (Pursuant to the CWA, jurisdictions report to EPA 

biannually on the condition of waters within their 

boundaries.)

http://www.epa.gov/owow/tmdl/2006IRG/report/2006irg-report.pdf

Elements of a State Water Monitoring and Assessment 

Program (EPA 841-B-03-003) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2003

This document recommends 10 basic elements of a state 

water monitoring program and serves as a tool to help EPA 

and states determine whether a monitoring program meets 

the prerequisites of CWA section 106(e)(1).

http://www.epa.gov/owow/monitoring/elements/

Consolidated Assessment and Listing Methodology (CALM): 

Toward a Compendium of Best Practices

Source: U.S. Environmental Protection Agency

Date of Publication: 2002

CALM provides a framework for states and other jurisdictions 

to document how they collect and use water quality data and 

information for environmental decision making. The primary 

purposes of the data analyses are to determine the extent to 

which all waters are attaining water quality standards, to 

identify waters that are impaired and need to be added to 

the 303(d) list, and to identify waters that can be removed 

from the list because they are attaining standards.

http://www.epa.gov/owow/monitoring/calm.html

Biological Criteria: Technical Guidance for Survey Design and 

Statistical Evaluation of Biosurvey Data

(EPA 822-B97-002) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1997

The emphasis of this guidance is on the practical application 

of basic statistical concepts to the development of biological 

criteria for surface water resource protection, restoration, 

and management.

http://www.epa.gov/bioindicators/pdf/EPA-822-B-97-002BiologicalCriteriaTechnicalGuidanceforSurveyDesignandStatisticalEvaluationofBiosurveyData.pdf

Generic Quality Assurance Project Plan Guidance for 

Programs Using Community Level Biological Assessment in 

Wadeable Streams and Rivers

(EPA 841-B-95-004) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1995

This document represents generic guidance for development 

of QAPPs for specific biological assessment projects or 

programs. It has been specifically designed for use by states 

using biological assessment protocols that focus on 

community-level responses as indicated by a multimetric 

approach and taxonomy to the genus/species level.

http://www.epa.gov/bioindicators/pdf/EPA-841-B-95-004GenericQualityAssuranceProjectPlanBioassessment.pdf
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 94

National Aquatic Resource Surveys:

National Coastal Condition Report. (2001) EPA-620/R-01/005 

National Coastal Condition Report II. (2004) EPA-620/R03/002 

Wadeable Streams Assessment. (2006) EPA-841-B-06-002 

National Coastal Condition Report III. (2008) EPA/842-R-08-

002 

National Lakes Assessment. (2010) EPA-841-R-09-001 

Source: U.S. Environmental Protection Agency

Dates of Publication: see above 

The surveys are conducted using a statistical survey design to 

yield unbiased, statistically representative estimates of the 

biological condition of the whole water resource (e.g., 

wadeable streams, lakes, rivers). Data are collected, 

processed, and analyzed through EPA-state collaboration to 

assess and report on the condition of the nation’s waters 

with documented confidence. Surveys collect a suite of 

indicators relating to the biological/physical habitat and 

water quality of the resource to assess the resource 

condition and determine the percentage meeting the goals of 

the CWA. Surveys collect information on biological and 

abiotic factors at 30–50 sites on an ecoregion level II scale for 

each resource.

http://www.epa.gov/owow/monitoring/nationalsurveys.html

http://www.epa.gov/owow/oceans/nccr/

http://www.epa.gov/owow/streamsurvey/

http://www.epa.gov/owow/lakes/lakessurvey/

Predictive Tools Description/summary

Landscape and Predictive Tools: A Guide to Spatial Analysis 

for Environmental Assessment (draft)

(EPA-100-R-11-002) 

Source: U.S. Environmental Protection Agency

Date of Publication: In process of finalization. Release

expected 2012.

This methods manual describes the purpose, rationale, and 

basic steps for using landscape and predictive tools for Clean 

Water Act monitoring, assessment, and management 

purposes such as filling monitoring gaps and prioritizing 

protection and rehabilitation actions. This guidance stresses 

simultaneous use of matched (or paired) landscape and in 

situ data for empirical modeling to enhance predictive 

capabilities and encourage science-based targeting and 

priority setting. Example and potential applications include 

criteria and standards development, problem identification 

and prevention, prioritization and targeting of rehabilitation, 

and advancing science, education, and society’s ability to 

effectively manage aquatic and terrestrial resources. This 

methods guidance is organized into four sections: (I) 

Introduction to Landscape and Predictive Tools; (II) 

Geographic Frameworks, Spatial Data, and Analysis Tools; (III) 

Examples and Case Studies; and (IV) Gaps and Needs for 

Research and Applications; plus an extensive Toolbox 

providing links to and short descriptions of a wide range of 

easily accessed data sets and analytical tools. Wider 

application of these tools and approaches should yield better 

protection for high-quality waters and quicker, more costeffective restoration of impaired waters.

http://www.epa.gov/raf/pubecological.htm

Stressor Response

Causal Analysis/Diagnosis Decision Information System 

(CADDIS)

Source: U.S. Environmental Protection Agency

Date: Last updated September 23, 2010

The Causal Analysis/Diagnosis Decision Information System, 

or CADDIS, is a website developed to help scientists and 

engineers in the Regions, States, and Tribes conduct causal 

assessments in aquatic systems. It is organized into five 

volumes:

• Volume 1: Stressor Identification

• Volume 2: Sources, Stressors & Responses

• Volume 3: Examples & Applications

• Volume 4: Data Analysis

• Volume 5: Causal Databases

http://www.epa.gov/caddis
A Primer on Using Biological Assessments to Support Water Quality Management

October 2011 95

Using Stressor-response Relationships to Derive Numeric 

Nutrient Criteria

(EPA-820-2-10-001) 

Source: U.S. Environmental Protection Agency

Date of Publication: 2010

This document provides guidance on statistical methods for 

estimating stressor-response relationships between changes 

in nutrient concentrations and changes in biological response 

variables. The document also provides guidance on methods 

for interpreting these relationships to derive numeric 

nutrient criteria. Other specific topics discussed include 

selecting appropriate covariates to improve the accuracy of 

estimated relationships, and methods for accounting for 

uncertainty in estimated relationships when deriving criteria.

http://water.epa.gov/scitech/swguidance/standards/criteria/nutrients/upload/finalstressor2010.pdf

Water quality-based toxics control Description/summary

Technical Support Document for Water Quality-based Toxics 

Control

(EPA-5052-90-001) 

Source: U.S. Environmental Protection Agency

Date of Publication: 1991

This document provides technical guidance for assessing and 

regulating discharge of toxic substances to waters of the 

United States. It was issued in support of EPA regulations and 

policy initiatives involving the application of biological 

assessment and chemical techniques to control toxic 

pollution to surface waters.

http://www.epa.gov/npdes/pubs/owm0264.pdf

Watershed Protection Description/summary

Identifying and Protecting Healthy Watersheds: A Technical 

Guide (draft) 

Source: U.S. Environmental Protection Agency

Date of Publication: In process of finalization. Release 

expected 2012.

This draft technical document provides an overview of the 

key concepts behind an approach to identify and protect 

healthy watersheds, examples of assessments of healthy 

watershed components, an integrated assessment 

framework for identifying healthy watersheds, examples of 

management approaches, sources of national data, and key 

assessment tools. It contains numerous examples and case 

studies from across the country. The intended audience for 

this document is aquatic resource scientists and managers at 

the state, tribal, regional, and local levels; non-governmental 

organizations; and federal agencies. It will also benefit local 

government land use managers and planners as they develop 

protection priorities.

http://water.epa.gov/polwaste/nps/watershed/index.cfm
Front cover:

1. Sampling in Rich Fork Creek, Davidson County, NC; Credit: Tetra Tech, Inc.

2. Yellow Perch, P. flavescens; Credit: U.S. Department of Agriculture

3. Adult Mayfly, Order: Ephemeroptera; Credit: Extension Entomology, 

Texas A&M University

4. Appalachian elktoe; Credit: Dick Biggins, U.S. Fish and Wildlife Service

5. Sailing in Carlyle Lake, IL; Credit: U.S. Army Corps of Engineers

6. Micrograph of freshwater diatoms; Credit: Algal Ecology Laboratory, Bowling 

Green State University

7. Coral Reef, St. Croix, USVI; Credit: Wayne Davis, U.S. Environmental Protection 

Agency

8. North River, Mount Crawford, VA; Credit: Tetra Tech, Inc.

9. Black-necked Stilt (Himantopus mexicanus), Maui, HI; 

Credit: John J. Mosesso, National Biological Information Infrastructure

Back cover:

10. Caddisfly; Credit: Rick Levey, Vermont Department of Environmental 

Conservation

11. California, salmon resting in a pool before resuming migration; 

Credit: U.S. Department of Agriculture, National Resources Conservation Service

12. Green River, UT; Credit: Scott T. Eblen, Medical University of South Carolina
EPA 810-R-11-01