The West River bordering New Haven and West Haven, Connecticut, is under evaluation for potential restoration of a former salt marsh. As part of a larger survey of biota associated with this river, the fish fauna was examined in the estuary and adjacent freshwaters. The results provide baseline data for monitoring restoration efforts and indicate the environmental health of the river. The fish communities lacked intolerant species, included significant numbers of individuals of non-native fishes, and showed low abundance and diversity of the native species, all indicating that this stretch of the river represents poor fish habitat with significant ecological disturbances. Some sites contained individuals with excessive parasites, tumors, ulcers, and fin erosion, which suggests physiological stress and potential human health hazards. These problems are localized in the vicinity of combined sewage outflows and/or storm sewer runoff from streets. They are exacerbated by periodic low flow or stagnant waters caused by the tide gates. Salt marsh restoration with tide-gate modification could improve habitat for species with commerical and recreational value and improve movement of diadromous fishes.