An official website of the United States government.

This is not the current EPA website. To navigate to the current EPA website, please go to This website is historical material reflecting the EPA website as it existed on January 19, 2021. This website is no longer updated and links to external websites and some internal pages may not work. More information »

Fact Sheet: Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance

On this page:


The U.S. Environmental Protection Agency (U.S. EPA) published technical guidance to help better protect and restore estuarine and coastal marine waters. This technical guidance 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. With the use of this guidance State/Tribal and Federal water resource managers will be able to better protect and restore the biological integrity of coastal and estuarine resources.


The objective of the Clean Water Act is to, "maintain and restore the chemical, physical, and biological integrity of our Nation's waters." Biological assessments and criteria, in addition to chemical, physical and toxicity criteria, are an important tool for maintaining and restoring the health of our waters.

Biological assessments can be conducted by a State or Tribe to determine the biological condition of a water body. When bioassessments are conducted at a number of unimpaired sites in similar water bodies, a reference condition is derived that describes the biological integrity of those water bodies. Using the reference condition, biocriteria can be established that will protect the desired biological condition of a specific water body.

Many natural resource agencies throughout the United States are using bioassessments and biocriteria for small rivers and streams and some States are beginning work in lakes and reservoirs. EPA issued guidance documents for these water bodies in 1996 and 1998, respectively (Biological Criteria: Technical Guidance for Streams and Small Rivers (EPA-822/B-96-001) and Lake and Reservoir Bioassessment and Biocriteria Technical Guidance Document (EPA 841-B-98-007)).

Bioassessments and biocriteria can be used to better understand the existing quality of the aquatic resources within a State or Tribal land; to define and protect aquatic life; to detect problems other water quality measurements may miss or underestimate; to help water resource managers set priorities for management; to assess the effectiveness of management actions and to track long term trends in water quality.


The guidance is a flexible compendium of methods for assessing estuaries, including options for defining reference conditions; a tiered sampling and assessment methodology, and several options for data analysis and index development. The methods comprise a flexible and versatile system for screening, detailed assessment, and diagnostic investigation.

A tiered sampling approach is described in the document, however, specific agency goals and objectives will determine the ultimate design of any biological sampling program. Tier 1 is a field screening requiring a single sampling of one biological assemblage, or group of organisms. Tier 2 is routine biological monitoring requiring at least two visits per year and sampling two biological assemblages. Tier 3 is comprehensive diagnostic investigation to determine causes of observed impairments.

Biological assessment in estuaries focus on assessing two key ecosystem components: the biota and their habitat. The condition of the biota depends on the quality of their habitat, including both physical and chemical quality. Habitat sampling and characterization in all tiers includes common mapped information as well as water column and substrate characterization.

Estuaries and coastal marine waters span a range of sizes from small sub-estuaries, embayments, and coastal lagoons to large estuaries and open coastal waters. A hierarchy of sizes is used to accommodate the potentially large range of estuary types that states may assess. The design of the sampling program should take these factors into consideration.

Sampling methods are derived from those commonly used along the coastal United States. Issues that need to be considered when sampling for biological assessment include: the assemblages that will be sampled, design strategies, and logistical considerations.

Sampling methods and candidate metrics are developed for four core groups of biological indicator assemblages: bottom dwelling organisms (benthic macroinvertebrates), fish, aquatic macrophytes, and phytoplankton. Three other indicator assemblages are under development: epibenthos, zooplankton, and paleoenvironmental reconstruction. The core assemblages are unambiguously useful for assessment; can be easily sampled and interpreted; and metrics are identified that can be used alone or in an index. Benthic macroinvertebrates have been most widely sampled, and are highlighted in this guidance document.

Reference conditions are expectations of the status of biological communities in the absence of anthropogenic disturbances and pollution. They reflect the biotic potential for estuaries and coastal marine waters. Reference conditions can be established with a combination of four elements: evaluation of historical data, sampling other reference sites, prediction using models, and expert consensus. In practice, most estuarine bioassessments have used reference sites and expert consensus. Criteria for reference sites may include absence of sediment contamination, absence of sediment or water column toxicity, no known dredging or spoil disposal, and dissolved oxygen meeting State criteria. Biocriteria development requires identification of natural factors that control the composition of biological assemblages. The most important factors affecting bottom-dwelling organisms are salinity, substrate (sediment) characterization, water depth, and biogeographic province.

Three alternative data analysis approaches for developing indexes for biocriteria are explained in the guidance: 1) an additive multimetric index; 2) a multivariate discriminant model to distinguish impaired sites from unimpaired sites; and 3) a pollution tolerance index from the species abundance found at a site. Finally, eight case studies illustrate the implementation of the methods.

Additional Information

Estuarine and Near Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance (EPA 822-B-00-024)

Top of Page