We sampled fish at eight locations in western Prince William Sound (PWS), Alaska, in April, July, and September 2006, and July 2007, to identify species assemblages and habitat use. At each location, fish were sampled with a 37-m long variable mesh beach seine in three nearshore habitats: bedrock outcrops, eelgrass meadows, and cobble beaches with kelp. A total of 49,060 fish representing 45 species were captured in 95 beach seine hauls. Catch-per-unit-effort (CPUE, all species) did not differ by season but did differ by habitat type—CPUE was greater in eelgrass and kelp than in bedrock. Seasonal pulses in catch were evident for some species; pink salmon were captured only in spring and summer, Pacific herring only in summer and fall, and capelin only in fall. Species richness was greater in summer (34) than in spring (23) or fall (28), and greater in eelgrass (34) than in bedrock (22) or kelp (33). Species that were good discriminators among seasonal collections were pink salmon, saffron cod, crescent gunnel, and Pacific herring, whereas species that were good discriminators among habitat collections were crescent gunnel, tubesnout, bay pipefish, saffron cod, and Arctic shanny. Of the most abundant species captured, most were juveniles based on estimated size at maturity. The summer fish assemblage in western PWS has changed over the last 20 years, especially with the appearance in large numbers of saffron cod. Sites in this study can be monitored periodically to track future changes in fish assemblages and habitat that may result from local and regional human disturbance.