Tolerance values provide a measure of the sensitivity of aquatic organisms to anthropogenic disturbance and have historically provided a useful tool for assessing the biological condition of streams and rivers. However, the tolerance values that are currently available are limited by the geographical areas in which they can be applied, and do not provide diagnostic information as to the causes of the impairment in streams. This report reviews and compares methods for estimating tolerance values from field data and for applying them to assess the biological condition of streams and to diagnose the causes of impairment. The intent of this report is to provide a resource of state, tribal, and regional biologists who wish to use tolerance values to help interpret biological data. Methods for estimating tolerance values first model (either explicitly or implicitly) the relationship between a given taxon and an anthropogenic stressor gradient (the taxonenvironment relationship). Then, a single representative value is extracted from this relationship, which is designated as the tolerance value. Three types of tolerance values are expressed on a continuous scale: (1) the weighted average, (2) cumulative percentiles, and (3) the maximum point of the taxon-environment relationship. A fourth type is categorical and classifies the shape of the taxon-environment relationship. All types of tolerance values provide fairly comparable rankings of tolerance among different taxa.