Spatial and temporal variability of fish assemblages in Nakaumi Lagoon along the Sea of Japan were studied using the seasonal catch data acquired by small set-net sampling from February to December 2008. We compared species composition and assemblage structures among different seasons and areas such as the sub-enclosed Honjo District and the outer Honjo District in the lagoon. A total of 10649 individuals representing 39 species were recorded, with Engraulis japonicus, Sardinella zunasi, Nuchequula nuchalis, Lateolabrax japonicus, Plecoglossus altivelis altivelis, Trachurus japonicas, Plotosus japonicus, and Konosirus punctatus being numerically dominant in the Lagoon. Species richness was greatest in summer due to the seasonal occurrence of temporary resident species including Sardinops melanostictus and Acanthopagrus schlegelii. In addition, the fact that the number of benthic species in summer was higher in the Honjo District than in the outer Honjo District, may have been a response to the relatively low level of hypoxia in the former.