Benthic invertebrates in streams include such animals as snails, mussels or clams, worms, leeches, and the larvae of many insects. Some invertebrates spend their entire lives in the stream while others like the insect larvae only begin their lives there. Some are tolerant of a wide variety of environmental conditions and others have a very narrow range of conditions they can tolerate. Benthic invertebrates don't move around much so they are good indicators of conditions at a particular site. Data on species, their abundances, their pollution tolerance and other environmental preferences, allow computation of metrics for water quality assessment in a manner similar to that used for algae and fish.

Two types of benthic invertebrate samples may be collected: a Qualitative Multihabitat (QMH) sample or a quantitative Richest-Targeted Habitat (RTH) sample. Qualitative samples are collected to provide a list of species found at a site. Quantitative samples are collected to provide actual abundances of species found in selected habitats at a site and allow computation of measures or metrics. The QMH sample is intended to represent species from as many different types of habitats as possible. The RTH sample is intended to represent the habitat with the greatest diversity of species, usually a riffle. In some streams, however, especially large rivers or sand-bottomed streams with no riffles, woody snags are sampled as the richest habitat.

Benthic invertebrate samples (RTH and QMH) were collected once annually from the four surface-water trends sites in Cycle II: Popple River , Duck Creek, Milwaukee River , and Lincoln Creek. Samples were collected from these same sites in Cycle I, and an examination of potential trends between Cycle I and Cycle II data may yield valuable information on changes in water quality at these sites. For example, samples were collected both before (1993-1995) and after (2003-2004) a large stream restoration effort at Lincoln Creek that was completed in 2002.

During low phase (starting in 2005), benthic invertebrate sampling will be limited to one RTH sample collected once annually from the Popple River site.

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