Rapid bioassessment is based on comparing habitat, water quality, and biological measures of a given stream with an expected state, or stream reference condition, that would exist in the same type of stream in the absence of human disturbance. Reference conditions are established by assessing "minimally" impaired stream sites, as it is rarely possible to find streams with no impairment at all. Reference sites should be established in good examples of the different types of streams found in the region. Regional reference characteristics represent the best attainable conditions for all streams with similar physical characteristics. The site-specific control is a segment of the stream being studied that represents the best attainable conditions for that stream.
Stream sites are classified into categories that would have similar aquatic communities under ideal conditions. The classification is based on characteristics that are intrinsic to the site (such as elevation, watershed size, stream gradient, soils, geology and other factors), not those resultant from human-induced change.
It is essential to classify stream sites before assessment, because comparing an assessed stream to a very different type of reference stream can lead to incorrect conclusions about condition. Comparing condition attributes between unlike sites is like comparing apples to oranges; the differences will have little relevant meaning. When the variance is partitioned so that similar sites are grouped together, the assessment and comparison is made more meaningful. The reference condition establishes the basis for making these comparisons and for detecting aquatic life impairment within each type of stream.
Because there are very few undisturbed streams left in the world, the establishment of the reference condition requires a decision on the "acceptability" of the reference sites after considering many criteria. The candidate reference sites should be assessed to determine their level of impairment relative to other sites in the geographic region. The characteristics of an acceptable "undisturbed" condition will likely vary from one region (and type of stream) to the next. The goal is to establish an expected condition that best represents the biological characteristics that you would anticipate finding in an undisturbed setting, acknowledging the limited information you may have about the past. When defining this expected condition, the physical characteristics of the region are key information. In addition to using reference sites, the reference condition is also based on historical data, empirical models, and expert opinion.