The Navarro River watershed hosts one of the last extant populations of coho salmon (Oncorhynchus kisutch) in the Central California Evolutionarily Significant Unit. As such, the identification and restoration of riparian habitats in the Navarro River watershed is paramount to the continued survival of this coho salmon population. This study utilizes a modeling procedure to identify priority locations in the Navarro River watershed using a geographic information system (GIS). This riparian habitat modeling method was used to identify priority restoration sites in the Navarro River watershed. The modeling structure emphasizes a hydrological metric, wetness index, and several landuse – land cover parameters. This GIS based model of the Navarro River was used for selecting potential riparian restoration sites, and used to demonstrate the utility of the model for selection of potential salmonid habitat. The results of analyzing the similarity between two model runs, one emphasizing habitat potential and the other anthropogenic degradation, indicate that riverine–riparian habitats have been disproportionately affected. This effort is offered as a potential tool to aid resource managers and local stakeholders with a method in which to initiate protection of aquatic ecological systems and coho salmon habitat in particular.