In recent years use of GIS natural resources databases has greatly improved watershed analysis techniques. These techniques have provided excellent inventories of watershed attributes supporting management strategies, but it has become evident that analysis techniques must include process-based assessments from the inventory data. Assessments must also include an integration of hydrology, geomorphology, and ecology observations. Protocols for process-based assessments are critical to achieving restoration project sustainability. The Kishwaukee River watershed, a 1,340-mi 2 watershed located in northern Illinois was chosen to test development of process-based protocols for watershed analysis. Stream power was found to be an important environmental driver correlating with physical habitat maintenance, recovery from stream channelization, and instream pollutant assimilation. The greatest impacts to ecological integrity appeared to be from rapid urbanization and agricultural practices in low-gradient subwatersheds. It was found that protocol development of ecological metrics could be greatly improved if bio-inventory data were consistently collected with respect to methodology and sample locations/times.