Keystone predators can impact many prey species, including those that are endangered. A requisite to assess the impact predators have on different prey populations is to identify the species being consumed in different types of communities, while accounting for possible seasonal variation in consumption. Here we used analysis of North American river otter (Lontra canadensis) scat to assess the impact river otters have on their prey populations, particularly endangered salmonids and migrating birds. We analyzed the prey composition of 1,411 river otter scats collected from 10 sites in Humboldt County, California, between 2011 and 2012. Analysis of prey items in scat placed study sites into four distinct clusters based on diet. Fish, mostly from the families Gasterosteidae, Cottidae, and Pholidae, formed the primary prey component, and crustaceans, birds, amphibians, and insects, also were important components of river otter diet. Salmonids constituted < 5% of overall diet, but river otters consumed the largest percentage of salmon during salmon spawning season at the inland cluster where salmonids spawn. Scat marking intensity varied between clusters and seasons, with the most scats collected in the autumn and the fewest in the winter/spring, except at the inland cluster where the pattern of marking activity was reversed. River otters may be responding to seasonal migrations of endangered and threatened salmonids. Diet surveys of this type are useful for monitoring resource use by top predators in aquatic ecosystems.