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The unit of sampling for ecological studies is the sampling reach, which is part of the stream where stream, bank, and flood-plain habitat features are representative of the local area, and near the fixed-site location where chemical data are collected. Three taxonomic groups- algae, invertabrates, and fish- are sampled because they respond differently to various environmental stresses.

Algae respond quickly to changes in their environment and serve as valuable biological indicators of rapid changes in water-resource conditions. The algal community is sampled from each of the habitats targeted for benthic invertebrates and a multihabitat composite sample also is prepared. All algal samples are collected in a semi-quantitative manner.

Benthic invertebrates (aquatic insects, mollusks, crustaceans, worms) have life cycles that are intermediate between fish and algae. They have close association with streambed sediments and can be used for characterizing changes in water quality over spatial areas. The types of benthic invertebrate samples collected in each sampling reach include semi-quantitative and qualitative.

Fish are valuable biological indicators of long-term water-resource conditions because they are long lived and have considerable economic value and public interest. Samples of the fish community are collected by using a combination of sampling methods, primarily electrofishing and seining.

In addition, habitat characterizations of channel, bank, and flood-plain features follow a spatial hierarchy that incorporates basin, stream segment, stream reach, and sample descriptors.