EPA scientists conduct research to develop and evaluate analytical methods for the identification, enumeration and evaluation of aquatic organisms exposed to environmental stressors and to correlate exposures with effects on chemical and biological indicators. Environmental measurements are required to determine the quality of ambient waters and the character of environmental stressors. Environmental stressors can include chemical pollutants, microbes and pathogens, physical agents such as land use, and processes such as alteration of wildlife habitat.

EPA’s scientists prepare and update field and laboratory protocol and methods manuals for stream and source monitoring indicators: fish, macroinvertebrates, periphyton, zooplankton, functional ecosystem indicators, water and sediment toxicity, and fish tissue contaminants. They also provide technical assistance to regions and states on the implementation and interpretation of these manuals. The current manuals and protocols prepared by EPA’s scientists are listed below.

Field Methods

• Field Operations Manual for Assessing the Hydrologic Permanence and Ecological Condition of Headwater Streams
• Environmental Monitoring and Assessment Program: Great River Ecosystems, Field Operations Manual 
• Logistics of Ecological Sampling on Large Rivers
• Comparisons of Boating and Wading Methods Used to Assess the Status of Flowing Waters
• Fish Field and Laboratory Methods for Evaluating the Biological Integrity of Surface Water
• Macroinvertebrate Field and Laboratory Methods for Evaluating the Biological Integrity of Surface Waters

Toxicity and Contaminant Methods

• A Compendium of Chemical, Physical and Biological Methods for Assessing and Monitoring the Remediation of Contaminated Sediment Sites
• A Survey of Fish Contamination in Small Wadeable Streams in the Mid-Atlantic Region.
• Stressor Identification Guidance Document
• Short-term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Waters to West Coast Marine and Estuarine Organisms
• Tropical Collector Urchin, Tripneustes gratilla, Fertilization Test Method
• Short-term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Water to Freshwater Organisms
• Short-term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Water to Marine and Estuarine Organisms
• Methods for Measuring the Acute Toxicity of Effluents and Receiving Waters to Freshwater and Marine Organisms