Recent work in river restoration and water resources management requires an expansion in scope to address the effects of watershed impairment. However, comprehensive investigations at watershed scales are made difficult by the limitations of existing data sets, which are often collected for analysis at much smaller scales. This is especially true of ecological and biological data that may be collected infrequently and for reach oriented studies. This research developed a protocol for assessing the changes in aquatic communities at the watershed scale. The first step in this protocol assembles biological assessment and monitoring data. The biological data is then used with an autecology matrix that provides opportunities for analysis of habitat, water quality, and other environmental factors that are species based. We have used this protocol to examine biological assessment data collected over two decades in the Kishwaukee River, Illinois. The protocol has provided a method to identify the effects of watershed modification as well as likely causes of existing conditions. This technique provides an improved understanding of historical influences on fish community structure by using a process-based assessment of historical data that integrates the state and condition of a biological community with likely environmental controls.