In two recent studies, North American river otters (Lontra canadensis) inhabiting the urbanized/industrialized harbors of southern Vancouver Island, British Columbia, Canada were found to be exposed to elevated levels of environmental contaminants, primarily industry-produced polychlorinated biphenyls (PCBs). Contaminant exposure in those studies was assessed non-invasively, by measuring chemical residue concentrations in river otter feces collected from established marking sites (latrines). As river otter exposure to contaminants is primarily through their diet, our aim was to characterize river otter prey selection from feces collected at latrine sites inside the contaminated harbors and along the relatively uncontaminated coastline outside the harbor systems. Fish occurred in 95.5% of all feces analyzed, with species of gunnels (Pholidae), sculpins (Cottidae), pricklebacks (Stichaeidae), toadfish (Batrachoididae), clingfish (Gobiesocidae), flatfish (Pleuronectiformes), and snailfish (Liparidae) being the most common prey consumed. Crustaceans were the only non-fish prey identified. Feces collected outside the harbors had a higher prevalence of pricklebacks, clingfish, and greenlings, whereas feces collected inside the harbor systems had a higher prevalence of toadfish and crustaceans. Because of the diversity of the river otter's diet, prey species from each of the main families described here should be analyzed for environmental contaminants to fully characterize concentrations of persistent compounds in the food-web. Prey sampling should be location-specific (i.e., inside and outside the urban/industrial harbors) to elucidate possible location effects on contaminant exposure.