Depth structures aquatic habitats, creating substantial differences in the species composition of underwater communities even at small intervals. Those communities also undergo considerable cyclic variation annually. In this study, we surveyed variation in the vertical distribution of fish in a shallow (20 m) coastal basin in the northern Baltic Sea during the ice-free period from May to October. The waters were strongly mixed throughout the season and only transient signs of stratification were observed. As production shifted towards higher trophic levels over summer, with sequential biomass peaks in zooplankton and juvenile fish, the vertical distribution of the entire fish assemblage became increasingly even. The results suggest that spatial resource partitioning can be strongly correlated with seasonal productivity cycles even in physically uniform environments with high connectivity. Further, the results stress the importance of sampling design (seasonal and vertical coverage) of fish studies in shallow coastal areas.