Biomonitoring is the process of inventorying aquatic organisms in a selected region of an aquatic system. All organisms have a tolerance level for pollutants. Tolerance levels vary from organism to organism. Thus, it is possible to determine at a point in time, qualitatively, the level of water quality impairment based on what fauna are present and their abundances. It is also possible to monitor changes in water quality by repeated sampling of the same areas over an extended period of time.
Habitat assessment is the process of evaluating the physical characteristics of a stream.
This is accomplished by quantifying parameters such as stream flow, depth, width, substrate type, bank stability and erosion potential, instream deposition and scour, and instream cover. These parameters and others provide important information about whether a habitat is suitable for various forms of aquatic life. These types of data, in conjunction with the fauna present, are also used to establish reference criteria for comparative purposes.