The major streams and rivers of the watershed were divided into segments, based primarily on geologic or geomorphic characteristics of the watershed portion where the streams were flowing. Each segment was further divided into reaches, based on various characteristics, such as stream gradient, riparian ecosystem type, and disturbance. In all, the project evaluated 17 segments comprised of 140 stream reaches.

During the assessment, project personnel conducted a field evaluation of each stream reach using established protocols, including the U.S. Environmental Protection Agency Rapid Bioassessment Protocols for physical stream habitat, the National Resource Conservation Service Riparian Habitat Assessment methods, and Bureau of Land Management Proper Functioning Condition procedures. These protocols allowed each reach to be given a score for in-stream and riparian habitat quality. Based on these scores, the riparian and in-stream habitat is placed into one of five habitat quality categories: high quality, slightly modified, moderately modified, heavily modified, and severely degraded. Each segment could then be mapped showing the stream and riparian habitat quality for every reach in the segment.