&EPA
A Primer on Using Biological Assessments
to Support Water Quality Management
October 2011
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I
The Hoopa Valley Tribe and neighboring tribes usetraditional redwood canoes for subsistence fishing
and ceremonial purposes.
U.S. Environmental Protection Agency
Office of Science and Technology
Office of Water, Washington, DC
EPA 810-R-11-01
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A Primer on Using Biological Assessments to Support Water Quality Management
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
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A Primer on Using Biological Assessments to Support Water Quality Management
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 Barren, 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
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A Primer on Using Biological Assessments to Support Water Quality Management
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 (Rl), 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 (RIO)
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 Mclntyre, 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
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
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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
Chapters. 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
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A Primer on Using Biological Assessments to Support Water Quality Management
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
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Table 3-5. Reference criteria for assessing biological integrity 46
Table 3-6. BMIBIand 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
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A Primer on Using Biological Assessments to Support Water Quality Management
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?
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.
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
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
Vulnerable 'Threatened * Lndanuered * Lxtinct Delisted
300 -
1979
1989
2008
Source: Jelks etal. 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 low-
level 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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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).
5.0%
National Biological Quality
Goo<1
Fair
Poor
Not Assessed
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.
http://water.epa.gov/tvpe/watersheds/monitoring/nationalsurveys.cfm.
http://water.usgs.gov/nawqa.
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A Primer on Using Biological Assessments to Support Water Quality Management
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, overtime 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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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 offish, 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
warmwaterfish species in the species sensitivity distribution from which a site-specific criterion is
calculated.
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A Primer on Using Biological Assessments to Support Water Quality Management
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
For an additional example, see
http://water.epa.gov/scitech/swguidance/waterqualitv/standards/criteria/aqlife/biocriteria/npdesmaryland.cfm.
5 http://www.dnr.state.md.us.
6 http://water.epa.gov/type/watersheds/monitoring/nationalsurvevs.cfm.
7 http://www.epa.gov/roe.
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A Primer on Using Biological Assessments to Support Water Quality Management
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
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
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stressors and toxicity effects. For example, Connecticut has developed a relationship between pollutant
loads, stormwater flows, and impervious land cover (1C) 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 1C 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)(l).
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.cfm7program id=45.
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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.cfm7program id=45.
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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.
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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.
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2.1 Tool #1: Biological Assessment Program Review
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/bioiwebl/html/keyconcepts.html
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.
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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.)
Attributes of levels of biological assessment program rigor
Key features
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; non-
random 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 intra-
regional 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, SQLServer, 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
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How rigorous
is my
program?
PROGRAM RIGOR
No Program
Level I
Level II
POTENTIAL PROGRAM
CAPABILITIES
Level III
None
Crude bioassessment
detects extremes
Pass-fail bioassessment
Three or more levels of
condition (e.g., excellent.
good, poor)
J I
EXAMPLE UPGRADE
ACTIVITIES
Establish biomonitoring using
critical technical elements
Upgrade method, sampling design;
develop method for measuring at
least one assemblage
Upgrade data analysis
methods
Develop method to measure
second assemblage
Level IV
Four or more levels of
condition (e.g., excellent,
good, fair, poor)
Program maintenance and
refinement, as needed
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.
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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 HUCto
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.
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2.2 Tool #2: The Biological Condition Gradient
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)
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).
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The Biological Condition Gradient:
Biological Response to Increasing Levels of Stress
Levels of Biological Condition
Level 1. Natural structural, functional,
and taxonomic integrity is preserved.
Level 2. Structure & function similar
to natural community with some
additional taxa & biomass; ecosystem
level functions are fully maintained.
Level 3. Evident changes in structure
due to loss of some rare native taxa;
shifts in relative abundance; ecosystem
level functions fully maintained.
Level 4. Moderate changes in structure
due to replacement of some sensitive
ubiquitous taxa by more tolerant
taxa; ecosystem functions largely
maintained.
Level 5. Sensitive taxa markedly
diminished; conspicuously unbalanced
distribution of major taxonomic groups;
ecosystem function shows reduced
complexity & redundancy.
Level 6. Extreme changes in structure
and ecosystem function; wholesale
changes in taxonomic composition;
extreme alterations from normal
densities.
Watershed, habitat, flow regime
and water chemistry as naturally
Chemistry, habitat, and/or flow
regime severely altered from
natural conditions.
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.
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• 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).
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A Primer on Using Biological Assessments to Support Water Quality Management
Table 2-2. Biological and other ecological attributes used to characterize the BCG.
Attribute
I. Historically documented,
sensitive, long-lived, or
regionally endemic taxa
II. Highly sensitive (typically
uncommon) taxa
I. Intermediate sensitive
and common taxa
IV. Taxa of intermediate
tolerance
V. Highly tolerant taxa
VI. Nonnative or
intentionally introduced
species
VII. Organism condition
VIII. Ecosystem function
IX. Spatial and temporal
extent of detrimental
effects
X. Ecosystem connectance
Description
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).
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).
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).
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).
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).
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.
Anomalies of the organisms; indicators of individual health (e.g., deformities, lesions, tumors).
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.
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.
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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BCG Calibration
A Primer on Using Biological Assessments to Support Water Quality Management
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, monsoon-
like 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.
Assemble Data
Data Analysis/Manipulation
Identify
Workshop
Participants
Calibration Workshop
Develop Decision Model
Test and
Review Model:
Adequate
Performance?
Yes
Calibrated BCG Model with
Narrative Decision Rules for
I Assigning Sample Sites to Tiers I
Figure 2-3. Steps in a BCG calibration.
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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
Total taxa
Highly Sensitive Taxa
(Attribute II only)
Richness of Sensitive Taxa
(combination of Attributes II
and lll,see table 2-2)
Abundance of Tolerant Taxa
(Attribute V)
Rules for BCG Level 2
Structure and function of community
similar to natural community with
some additional taxa and biomass
More than 12 taxa
More than two taxa
Attribute II + Attribute III are more
than 50% of total taxa richness
Abundance of Attribute V is less than
20% of community
Rules for BCG Level 3
Evident changes in structure due to
loss of some rare native taxa; shifts in
relative abundance
More than 12 taxa
May be absent
Attribute II + Attribute III are more
than 35% of total taxa richness
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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 20* 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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A Primer on Using Biological Assessments to Support Water Quality Management
2.3 Tool #3: Stressor Identification (SI) and Causal Analysis/Diagnosis Decision
Information System (CADDIS)
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
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
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
I Detect or Suspect Biological Impairment
Decision-maker
and Stakeholder
Involvement
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
Stressor Identification
DEFINE THE CASE
LIST CANDIDATE CAUSES
EVALUATE DATA FROM THE CASE
EVALUATE DATA FROM ELSEWHERE
IDENTIFY PROBABLE CAUSE
As Necessary:
Acquire Data, and
Iterate Process
Identify and Apportion Sources
MANAGEMENT ACTION:
Eliminate or Control Sources,
Monitor Results
I Biological Condition Restored or Protected I
Source: USEPA2010b
Figure 2-4. Stressor identification process.
-
-
-I
(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.
http://cfpub.epa.gov/caddis/index.cfm.
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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
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A Primer on Using Biological Assessments to Support Water Quality Management
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.
ENVIRONMENTAL
MONITORING
INFORMATION
INTEGRATED
DECISION-MAKING
ENVIRONMENTAL
OUTCOMES
• improve degraded
conditions?
• protect our high
quality waters?
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
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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A Primer on Using Biological Assessments to Support Water Quality Management
3.1 Protecting Water Quality Improvements and High Quality Conditions in Maine
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).
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.
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A Primer on Using Biological Assessments to Support Water Quality Management
Table 3-1. Criteria for Maine river and stream classifications and relationship to antidegradation
policy.
Class
AA
A
B
C
Dissolved
oxygen
criteria
As naturally
occurs
7 ppm; 75%
saturation
7 ppm; 75%
saturation
5 ppm; 60%
saturation;
and
6.5 ppm
(monthly
avg.) when
temperature
is
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A Primer on Using Biological Assessments to Support Water Quality Management
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 TA 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
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.
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
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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.
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.
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
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condition and less than the 25* 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
Greater than or equal to the 25th percentile of reference condition
Greater than the 10th and less than the 25th percentile of reference
condition
IBI scores
coldwater
>52
46-51
warmwater
>50
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
Abstract
Maryland is identifying high-quality waters for antidegradation purposes on a waterbody-
by-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.
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-by-
waterbody 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(6)].
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.
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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
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.
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., low-
gradient 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.
J
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
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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A Primer on Using Biological Assessments to Support Water Quality Management
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 (non-
reference 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.
score
DQ
100
90
80
70
60
50
40
30
20
10
0
oo
8
X X
X
p
X
xx
0*0
o A: reference
x B: non-reference
D C: moderately stressed
O D: heavily stressed
OB
*«*
i
3
I
4
BCG level assignement
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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A Primer on Using Biological Assessments to Support Water Quality Management
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
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.
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
Coldwater habitat (CWH)
Exceptional warmwater habitat (EWH)
Seasonal salmonid habitat (SSH)
Warmwater habitat (WWH)
Limited warmwater habitat (LWH)
Modified warmwater habitat (MWH)
Limited resource water (LRW)
Key attributes
Native cold water or cool water species; put and take trout stocking.
Unique, unusual, and highly diverse assemblage offish and
invertebrates.
Supports lake run steelhead trout fisheries.
Typical assemblages of fish and invertebrates, similar to least impacted
reference conditions.
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.
More tolerant assemblages offish 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.
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.
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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 Well-
Being [Mlwb]) 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 beatable 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 overtime 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
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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
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.
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.
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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.
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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
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.
J
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 offish (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.
Under the CWA, class B waters are designated for the protection of aquatic life uses. The WW-2 classification is
for small streams.
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Table 3-4. Qualitative scoring guidelines for the BMIBI and FIBI.
Biological Condition Rating (BCR)
Poor
Fair
Good
Excellent
BMIBI
0-30
31-55
56-75
76-100
FIBI
0-25
26-50
51-70
71-100
Source: http://www.iowadnr.gov/Environment/WaterQualitv/Watershedlmprovement/WatershedResearchData/
WaterlmprovementPlans/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.
Ecoregion3
52B Ref. (Paleozoic Plateau)
47C Ref. (lowan Surface)
BMIBI
61
59
FIBI
59
71 (riffle), 43 (non-riffle)
Source: http://www.iowadnr.gov/Environment/WaterQuality/Watershedlmprovement/WatershedResearchData/
WaterlmprovementPlans/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 lowan 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
REMAP 147
TMDL 28
TMDL 28
New Wine Park
TMDL 29
TMDL 30
TMDL 30
H2
Year
2005
2001
2005
1999
2001
2001
2005
1999
BMIBI
42 (Fair)
47 (Fair)
26 (Poor)
N/Aa
47 (Fair)
51 (Fair)
48 (Fair)
53 (Fair)
FIBI
34(Fair)
29 (Fair)
37 (Fair)
32
26 (Fair)
33 (Fair)
7 (Poor)
37 (Fair)
Modified from http://www.iowadnr.gov/Environment/WaterQualitv/Watershedlmprovement/
WatershedResearchData/WaterlmprovementPlans/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."]
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
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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
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 (1C) with benthic macroinvertebrate data collected from wadeable
streams was conducted, and results showed that the designated aquatic life use was not
supported when 1C was more than 12 percent of the watershed area. A TMDL was
developed in 2007 using a target of 12 percent 1C—the first in the nation to use 1C as a
surrogate for stormwater. Objectives to reduce 1C 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.
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 (1C)
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 1C 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 1C. 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 1C was calculated for each. For each segment, a TMDL implementation objective was also developed
(Table 3-7).
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Table 3-7. Summary of TMDL analysis for Eagleville Brook.
Waterbody segment
From the mouth at Eagleville Pond upstream to
the confluence with Kings Brook, Mansfield
The confluence with Kings Brook to headwaters
near UCONN campus
Unnamed pond on UCONN campus
TMDL target
12%
12%
12%
1C
5%
14%
27%
Implementation objective
Antidegradation
21% reduction in the percent 1C
59% reduction in the percent 1C
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 1C 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 1C, 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 1C has been developed. Considerable
stakeholder input has crafted a consensus approach to seize opportunities to reduce the effect of 1C 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 1C, as
well as flow monitoring to determine whether changes in 1C 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 1C in the Eagleville Brook watershed. Additional information on the
implementation of the Eagleville Brook TMDL can be found at
http://clear.uconn.edu/proiects/tmdl/index.htm.This site, hosted by UCONN, provides additional
information and will be used to track the progress of TMDL implementation overtime.
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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
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.
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 (u.g/L). This level would have resulted in an
instream concentration of 36 u.g/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 pollutant-
tolerant 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
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(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
Facility A
Facility B
Flow
monthly average
150,000 gal/day
35,000 gal/day
Copper
Monthly average
0.027 Ib/day
0.007 Ib/day
Daily maximum
0.038 Ib/day
0.0125 Ib/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 Ib/day, at concentration of 0.8 mg/L monthly average.
Northfield treatment plant copper effluent limitations were also established at 0.26 Ib/day monthly
average and 0.36 Ib/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 (Bl) 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
Assess
(criteria)
Density
(> 300)
Richness
(>30)
EPT
(>18)
Bl
(< 5.00)
Ept/EptC
(>0.45)
1993
Fair
1,862
39
12
4.73
0.029
1994
Fair
3,282
43
16
4.74
0.50
1995
Fair
1,037
41
16
4.61
0.52
2000
Fair-Poor
4,556
50
14
5.51
0.29
2001
Poor
5,640
50
11
6.00
0.07
2003
Poor
4,264
62
22
5.26
0.22
2004
Poor
668
34
12
5.12
0.14
2005
Very
Good
2,160
51
28
4.38
0.89
2006
Excellent
5,870
62
33
3.48
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
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.
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 offish 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 EPTtaxa (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
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some of the stream's riparian buffer and instream habitat (Table 3-10). However, only 27 percent of the
total taxa were EPTtaxa, which is much lower than the 60-75 percent proportion of EPTtaxa expected
in unimpacted or minimally impacted streams in this area. Increases in EPTtaxa 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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Table 3-10. Sampling to assess progress toward restoration goals.
Parameter
Turbidity
Dissolved oxygen
Number of
macroinvertebrates
% diptera
% EPT species
Pre-restoration sampling
results (year)
12.3 NTU (1997)
6.3 mg/L (2000)
27 (2000)
10 (2004)
29.6% (2004)
27% (2004)
Restoration goal
50% reduction
2 mg/L increase
200
Reduction to 5% of total
Increase to 60% of total
Post-restoration sampling
results (year)
2.4 NTU (2009)
9.6 mg/L (2009)
350 (2008)
1.3% (2008)
30% (2009)
Table 3-11. Plant sampling results.
Parameter
Number of plant taxa
FQI score
Number of invasive plant species
Number of sensitive or rare taxa
2004
13
14
3
0
2008
21
19
3
3
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3.11 Using Biological Assessment Data to Show Impact of NFS Controls in
Michigan
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.
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.
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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
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.
J
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.
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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
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.
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, high-
quality 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
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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
(USAGE 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
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.
In 2003 Virginia Commonwealth University's Center for Environmental Studies, Virginia Department of
Conservation and Recreation (VA OCR), 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
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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 (mlBI) 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 OCR, 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
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.
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, EPTtaxa 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 EPTtaxa was largely driven by losses of
coldwater-preference EPTtaxa, but in some cases it was also influenced by gains in warm-preference
EPTtaxa.
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 EPTtaxa
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
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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 DEQuses 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
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.
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 community-
level 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/tvpe/oceb/assessmonitor/nccr/index.cfm.
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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 two-
dimensional (2-D) live coral cover, EPA has developed a rapid survey procedure for estimating three-
dimensional (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 Guanica 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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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.
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.
S 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.
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
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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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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
Abstract
Assessment of biological conditions in Oregon's Coast Coho Evolutionary 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.
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 Evolutionary
Significant Unit (ESU). The Oregon Coast Coho ESU is in western Oregon, spanning approximately three-
quarters 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.
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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
Least disturbed
Moderately disturbed
Most disturbed
O/E
>0.91
0.86-0.91
<0.86
Taxa loss
8% or less
9%-14%
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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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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Numeric Nutrient Criteria. EPA-820-2-10-001. U.S. Environmental Protection Agency.
. Accessed September 2011.
USEPA (U.S. Environmental Protection Agency). 2010b. Causal Analysis/Diagnosis Decision Information
System (CADDIS). Office of Research and Development, Washington, DC.
. 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.
. 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.
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. . 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.
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Glossary
aquatic assemblage
aquatic community
aquatic life use
attribute
benthic macroinvertebrates or
benthos
best management practice
biological assessment or
bioassessment
biological criteria or biocriteria
biological indicator or bioindicator
biological integrity
biological monitoring or
biomonitoring
biological survey or biosurvey
An association of interacting populations of organisms in a
given waterbody; for example, fish assemblage or a benthic
macroinvertebrate assemblage.
An association of interacting assemblages in a waterbody, the
biotic component of an ecosystem.
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.
The measurable part or process of a biological system.
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.
An engineered structure or management activity, or
combination of those, that eliminates or reduces an adverse
environmental effect of a pollutant.
An evaluation of the biological condition of a waterbody using
surveys of the structure and function of a community of
resident biota.
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.
An organism, species, assemblage, or community characteristic
of a particular habitat, or indicative of a particular set of
environmental conditions.
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.
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.
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
Clean Water Act
Clean Water Act 303(d)
Clean Water Act 305(b)
criteria
designated uses
disturbance
ecological integrity
ecoregion
function
guild
An area that is relatively uniform in physical structure and that
is identified by a dominant biota.
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 etseq.
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.
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.
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.
Those uses specified in WQS for each waterbody or segment
whether or not they are being attained.
Human activity that alters the natural state and can occur at or
across many spatial and temporal scales.
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.
A relatively homogeneous ecological area defined by similarity
of climate, landform, soil, potential natural vegetation,
hydrology, or other ecologically relevant variables.
Processes required for normal performance of a biological
system (may be applied to any level of biological organization).
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
index of biological/biotic integrity
invasive species
least disturbed condition
maintenance of populations
metric
minimally disturbed condition
multimetric index
narrative biological criteria
native
Data sets from previous studies, which can range from
handwritten field notes to published journal articles.
An integrative expression of site condition across multiple
metrics; an IBI is often composed of at least seven metrics.
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].)
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.
Sustained population persistence; associated with locally
successful reproduction and growth.
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.
The physical, chemical, and biological conditions of a
waterbody with very limited, or minimal, human disturbance.
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).
Written statements describing the structure and function of
aquatic communities in a waterbody that support a designated
aquatic life use.
An original or indigenous inhabitant of a region; naturally
present.
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nonnative or intentionally
introduced species
numeric biological criteria
periphyton
rapid bioassessment protocols
reference condition (biological
integrity)
reference site
refugia
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.
Specific quantitative measures of the structure and function of
aquatic communities in a waterbody necessary to protect a
designated aquatic life use.
A broad organismal assemblage composed of attached algae,
bacteria, their secretions, associated detritus, and various
species of microinvertebrates.
Cost-effective techniques used to survey and evaluate the
aquatic community to detect aquatic life impairments and their
relative severity.
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
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.
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
sensitive or regionally endemic
taxa
sensitive - rare taxa
sensitive - ubiquitous taxa
stressors
structure
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.
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 long-
lived, 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.
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.
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.
Physical, chemical, and biological factors that adversely affect
aquatic organisms.
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.
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
tolerant taxa
total maximum daily load
toxicity identification evaluation
toxicity reduction evaluation
water quality management
(nonregulatory)
water quality standard
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.
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.
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.
A set of procedures to identify the specific chemicals
responsible for effluent toxicity.
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.
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.
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
BCG
BMIBI
BMP
CADDIS
CTDEP
CWA
CWH
EPA
EPT
ESU
EV
EWH
FIBI
FQI
FSS
GIS
GPS
HQ
HUC
IBI
1C
ICI
IDNR
INSTAR
IRG
LRW
LWH
MDE
MDEQ
MDNR
MEDEP
mlBI
Mlwb
MPCA
MWH
NARS
NAWQA
NBEP
Arizona Department of Environmental Quality
biological condition gradient
benthic macroinvertebrate index of biotic integrity
best management practice
Causal Analysis/Diagnosis Decision Information System
Connecticut Department of Environmental Protection
Clean Water Act
coldwater habitat
U.S. Environmental Protection Agency
ephemeroptera, plecoptera, trichoptera taxa
evolutionary significant unit
exceptional value (Pennsylvania)
exceptional warmwater habitat
fish index of biotic integrity
Floristic Quality Index
fine sediment stress
geographic information system
global positioning system
high-quality (Pennsylvania)
hydrologic unit code
index of biological/biotic integrity
impervious cover
invertebrate community index
Iowa Department of Natural Resources
Interactive Stream Assessment Resource
Integrated Reporting Guidance
limited resource water
limited warmwater habitat
Maryland Department of the Environment
Michigan Department of Environmental Quality
Maryland Department of Natural Resources
Maine Department of Environmental Protection
modified index of biological integrity
modified index of well-being
Minnesota Pollution Control Agency
modified warmwater habitat
National Aquatic Resource Surveys
National Water-Quality Assessment
Narragansett Bay Estuary Program
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NEP
NFMR
NJ DEP
NOAA
NPDES
NPS
NTU
NWQC
0/E
ODEQ
ODFW
ONRW
ORD
PA DEP
PREDATOR
QHEI
RIVPACS
SI
SSH
TBEP
TIE
TMDL
TRE
TS
UAA
UCONN
USGS
UTDEQ
VADCR
VSA
VTDEC
WET
WQL
WQS
WWH
WWTF
WWTP
National Estuary Program
North Fork Maquoketa River
New Jersey Department of Environmental Protection
National Oceanic and Atmospheric Administration
National Pollutant Discharge Elimination System
nonpoint source
nephelometric turbidity unit
numeric water quality criteria
observed over expected
Oregon Department of Environmental Quality
Oregon Department of Fish and Wildlife
Outstanding National Resource Water
Office of Research and Development (U.S. Environmental Protection Agency)
Pennsylvania Department of Environmental Protection
PREDictive Assessment Tool for Oregon
qualitative habitat evaluation index
River Invertebrate Prediction and Classification System
stressor identification
seasonal salmonid habitat
Tampa Bay Estuary Program
toxicity identification evaluation
Total Maximum Daily Load
toxicity reduction evaluation
temperature stress
use attainability analysis
University of Connecticut
U.S. Geological Survey
Utah Department of Environmental Quality
Virginia Department of Conservation and Recreation
Virtual Stream Assessment
Vermont Department of Environmental Conservation
whole effluent toxicity
water quality limited
water quality standards
warmwater habitat
wastewater treatment facility
wastewater treatment plant
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Appendix A. Additional Resources
Biological Assessment and Biological Criteria: Technical Guidance
Biological assessment and biological criteria
Biological Criteria: National Program for Surf ace Waters
(EPA 440-5-90-004)
Source: U.S. Environmental Protection Agency
Date of Publication: 1990
Description/summary
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 chemical-
specific analysis and whole effluent and ambient toxicity
testing methods in the water quality program.
http://www.epa.gov/bioiwebl/pdf/PolicyonBiologicalAssessmentsandCriteria.pdf
Coral reefs
Stony Coral Rapid Bioassessment Protocol
(EPA600-R-06-167)
Source: U.S. Environmental Protection Agency
Date of Publication: 2007
Description/summary
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?dirEntryld=223392
Estuaries and coastal waters
Estuarine and Coastal Marine Waters: Bioassessment and
Biocriteria Technical Guidance
(EPA822-B-00-024)
Source: U.S. Environmental Protection Agency
Date of Publication: 2000
Description/summary
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
Lakes and Reservoir Bioassessment and Biocriteria Technical
Guidance Document
(EPA841-B-98-007)
Source: U.S. Environmental Protection Agency
Date of Publication: 1998
Description/summary
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
Concepts and Approaches for the Bioassessment of Non-
wadeable Streams and Rivers
(EPA600-R-06-127)
Source: U.S. Environmental Protection Agency
Date of Publication: 2006
Description/summary
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
Biological Criteria: Technical Guidance for Streams and Small
Rivers
(EPA822-B-96-001)
Source: U.S. Environmental Protection Agency
Date of Publication: 2001
Description/summary
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-TechnicalGuidanceforStreamsandSmallRivers-
revisededitionl996.pdf
Rapid Bioassessment Protocols for Use in Streams and
Wadeable Rivers: Periphyton, Benthic Macroinvertebrates
and Fish, 2nd ed.
(EPA841-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
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
Description/summary
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
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
Description/summary
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)(l).
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
(EPA822-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-97-002BiologicalCriteria-
TechnicalGuidanceforSurveyDesignandStatisticalEvaluationofBiosurveyData.pdf
Generic Quality Assurance Project Plan Guidance for
Programs Using Community Level Biological Assessment in
Wadeable Streams and Rivers
(EPA841-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-95-004GenericQualitvAssuranceProiectPlanBioassessment.pdf
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National Aquatic Resource Surveys:
National Coastal Condition Report. (2001) EPA-620/R-01/005
National Coastal Condition Report II. (2004) EPA-620/R-
03/002
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
http://www. eDa.gov/owow/monitoring/nationalsurvevs. html
http://www.epa.gov/owow/oceans/nccr/
http://www.epa.gov/owow/streamsurvey/
http://www.epa.gov/owow/lakes/lakessurvev/
Predictive Tools
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.
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.
Description/summary
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: (1)
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 cost-
effective 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
October 2011
94
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A Primer on Using Biological Assessments to Support Water Quality Management
Using Stresses-response Relationships to Derive Numeric
Nutrient Criteria
(EPA-820-2-10-001)
Source: U.S. Environmental Protection Agency
Date of Publication: 2010
This document Drovides guidance on statistical methods for
estimating stressor-resDonse relationshiDs between changes
in nutrient concentrations and changes in biological resDonse
variables. The document also Drovides guidance on methods
for interDreting these relationshiDs to derive numeric
nutrient criteria. Other SDecific toDics discussed include
selecting aDDroDriate covariates to imDrove the accuracy of
estimated relationshiDs, and methods for accounting for
uncertainty in estimated relationshiDs when deriving criteria.
htto://water.e Da.gov/scitech/swguidance/standards/criteria/nutrients/UDload/finalstressor2010.Ddf
Water quality-based toxics control
Technical Support Document for Water Quality-based Toxics
Control
(EPA-5052-90-001)
Source: U.S. Environmental Protection Agency
Date of Publication: 1991
Description/summary
This document Drovides technical guidance for assessing and
regulating discharge of toxic substances to waters of the
United States. It was issued in suDD°rt of EPA regulations and
Dolicy initiatives involving the aDD'ication of biological
assessment and chemical techniques to control toxic
Dollution to surface waters.
httD://www. eDa.gov/nDdes/Dubs/owm0264.Ddf
Watershed Protection
Identifying and Protecting Healthy Watersheds: A Technical
Guide (draft)
Source: U.S. Environmental Protection Agency
Date of Publication: In Drocess of finalization. Release
exDected 2012.
Description/summary
This draft technical document Drovides an overview of the
key conceDts behind an approach to identify and Drotect
healthy watersheds, examDles of assessments of healthy
watershed comDonents, an integrated assessment
framework for identifying healthy watersheds, examDles of
management aDDroaches, sources of national data, and key
assessment tools. It contains numerous examDles 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 Dinners as they develoD
Drotection Driorities.
httD://water.eDa.gov/Dolwaste/nDS/watershed/index.cfm
October 2011
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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
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&EPA
EPA810-R-11-01
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