Eelgrass Zostera marina can form extensive meadows on Puget Sound river deltas. The extent to which these meadows provide critical rearing habitat for local estuarine fishes, especially out‐migrating juvenile salmon, is not well understood. Further, delta eelgrass has been impacted by diking and river channelization with unknown consequences for fish. We sampled fish in the Skagit River delta, Washington, during April–September with a lampara net, which is well suited to capturing fish in eelgrass. We compared abundance and body size of Chinook Salmon Oncorhynchus tshawytscha and three forage fish species between eelgrass and nearby unvegetated habitat. We also assessed combined effects of eelgrass characteristics (meadow size and morphology) and oceanographic conditions (temperature and salinity), which covaried according to proximity and orientation to channelized distributary outlets, diked shorelines, and a jetty. Chinook Salmon were more abundant in eelgrass than in unvegetated habitat in June–July and were relatively more abundant in eelgrass compared with unvegetated habitat in regions with intact eelgrass than offshore from a channelized distributary outlet. Abundances of Pacific Herring Clupea pallasii and Shiner Perch Cymatogaster aggregata were consistently severalfold higher in eelgrass than in unvegetated habitat. Surf Smelt Hypomesus pretiosus were more abundant in eelgrass than in unvegetated habitat at some locations, but never less abundant in eelgrass. Our results suggest that conservation and restoration of delta eelgrass would benefit these species and help to identify the settings in which these actions would be most beneficial.