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Biological Assessment - Technical Assistance Documents for States, Tribes and Territories

The EPA provides technical support for states and tribes as they develop biological criteria and biological assessment programs. Some technical assistance is applicable to all water bodies in general, and other technical assistance targets specific types of water bodies.

On this page:

Technical Assistance Applicable to All Water Bodies

2016 Practitioner’s Guide to the Biological Condition Gradient: A Framework to Describe Incremental Change in Aquatic Ecosystems

This EPA technical support document provides a scientific framework, the Biological Condition Gradient (BCG), for states, territories and tribes to describe incremental biological change along a gradient of stress from undisturbed to highly disturbed conditions. The document also describes the steps for developing a quantitative BCG based on over 10 years of piloting with states and other partners. The BCG can be used to interpret biological responses from the cumulative effects of stressors and measure changes in biological condition. In conjunction with other biological indicators and assessment methods, this tool can also be used to help identify high quality waters, track improvements in degraded waters, and develop numeric biological criteria.

2013 Biological Assessment Program Review: Assessing Level of Technical Rigor to Support Water Quality Management

This EPA document provides a process for states and tribes to evaluate the technical rigor and breadth of capabilities of a biological assessment program. Using the program review process described in this document, states and tribes can identify the technical capabilities and the limitations of their biological assessment programs and develop a plan to build on the program strengths and address the limitations.

2011 Primer on Using Biological Assessment to Support Water Quality Management

This EPA 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.

2000 Stressor Identification Guidance

The EPA Stressor Identification (SI) Guidance leads 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 ability to accurately identify stressors and defend the evidence supporting those findings is a critical step in developing strategies that will improve the quality of aquatic resources.

1992 Procedures for Initiating Narrative Biological Criteria

This guidance document describes EPA expectations regarding the development of narrative biological criteria, and helps to clarify and support the term narrative biological criteria as presented on the 1990 Biological Criteria National Program Guidance for Surface Waters. This document summarizes in a simple and easy to understand manner the historical background to biological criteria; the linkage between biological integrity and reference; the use of reference as the goal to define and protect aquatic life uses, inform attainment decisions, and follow up regulatory actions. This document provides information on what is necessary to develop a narrative biological criterion –including and example- and recommends quantitative information to be incorporated into the assessment phase and eventually into a numeric criterion.

1990 Biological Criteria: National Program Guidance for Surface Waters

This EPA document provides guidance for development and implementation of narrative biological criteria. More recent guidance documents on this page provide additional technical information to facilitate development and implementation of narrative and numeric criteria for each of the surface water types.


Technical Assistance for Lakes and Reservoirs

1998 Lake and Reservoir Bioassessment and Biocriteria: Technical Guidance Document

This EPA guidance document provides a tool to assist lake managers in using scientifically valid, practical biological assessment in the management of the Nation's lakes and reservoirs. The guidance was developed based on the experiences of existing state, regional and national lake monitoring programs, some of which are cited in case studies throughout the document.


Technical Assistance for Streams and Wadeable Rivers

2013 USGS Publication: Analytical Approaches Used in Stream Benthic Macroinvertebrate Biomonitoring Programs of State Agencies in the United States

This report by the US Geological Survey provides a summary of different analytical approaches used in benthic macroinvertebrate monitoring across the US.

1999 Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers

This EPA document provides rapid bioassessment protocols that can be used to provide basic aquatic life data for water quality management purposes such as problem screening, site ranking, and trend monitoring.

1996 Biological Criteria: Technical Guidance for Streams and Small Rivers

This EPA guidance document is designed 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.


Technical Assistance for Estuaries and Near Coastal Waters

2000 Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance

This EPA document provides an extensive collection of methods and protocols for conducting bioassessments in estuarine and coastal marine waters and the procedures for deriving biocriteria from the results. Several case studies illustrate the bioassessment process and biocriteria derivation procedures.


Technical Assistance for Wetlands

2002 Methods for Evaluating Wetland Condition

Several EPA documents have been published to support the National Nutrient Strategy by providing states and tribes with methods to assess waterbody nutrient impairment and develop ecoregion-specific nutrient criteria.

The wetlands modules are a starting point to help states and tribes establish biological and nutrient water quality criteria specifically refined for wetlands. Below are links to the biological criteria-related documents in the wetlands modules. 

Biological Criteria-Related Modules:

1998 Wetlands Bioassessment Fact Sheets

This is a series of ten fact sheets describing how States and Tribes can develop biological criteria and conduct biological assessments in wetlands.


Technical Assistance for Coral Reefs

2014 Workshop on Biological Integrity of Coral Reefs

This report summarizes an EPA-sponsored workshop in coral reef biological integrity held at the Caribbean Coral Reef Institute in La Parguera, Puerto Rico in 2012. During this workshop experts evaluated photos and videos of EPA coral reef surveys and discussed the reef attributes that characterize biological integrity for these systems. In the long-term this work is expected to inform and provide a well-defined narrative for scientifically defensible thresholds for different levels of coral reef condition.

2010 Coral Reefs Biological Criteria: Using the Clean Water Act to Protect a National Treasure

This document provides assistance to coral reef managers on how to use the Clean Water Act and coral reef biological criteria as part of a comprehensive framework to organize their protection efforts. 

2007 Stony Coral Rapid Bioassessment Protocol

EPA's Stony Coral Rapid Bioassessment Protocol is an inexpensive, no-contact, non-technical underwater survey procedure designed for jurisdictions with coral expertise but limited funding and personnel. The protocol focuses only on scleractinian (stony) reef-building corals because of their fundamental importance to coral reef ecology and ecosystem value. This focus provides vital information for reef assessment and provides a strong foundation for characterization of other reef attributes.

2006 Bioassessment Tools for Stony Corals

EPA conducted a biological survey in St. Croix, U.S. Virgin Islands to inform and calibrate a long-term monitoring strategy for development of coral reef biocriteria. Data from the biological survey were used to validate metrics and the approach described in the 2007 Stony Coral Rapid Bioassessment Protocol (above). The three supporting EPA publications are below:

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