Fish assemblages on an Eelgrass (Zostera marina) bed located in Humboldt Bay, California were studied using an epibenthic otter trawl. Sampling was conducted on a monthly basis from 1994 to 1995, and 2003 through 2006. A total of 204 tows over 51 mo yielded 16,760 individual fish representing 20 families and 43 species. The catch was dominated by a few species, with 4 species comprising 74.3% of the total number of fish collected. Black Rockfish (Sebastes melanops) were the most abundant species taken, accounting for 22.5% of the total collected. Annual peaks in abundance and species richness were observed during the late spring and summer months, with smaller peaks noted in winter. Fish assemblages differed seasonally, with late spring and summer assemblages significantly different from other times of the year, due to recruitment of young-of-the-year life stages. Temporal patterns of community structure were also analyzed by decade and season, with no interaction among main effects. Seasonal and temporal patterns were analyzed using permutational multivariate analysis of variance and plotted using nonmetric multidimensional scaling. These results demonstrate the importance of Eelgrass habitats to juvenile fishes, and the value of data sets collected over various temporal scales.