We studied seasonal and small-scale spatial variation in fish assemblage structure in the northern Baltic Proper archipelago. The study was conducted in a shallow coastal basin during three consecutive production-seasons. The structure of the fish assemblage changes significantly seasonally, from early summer (May-June) to late summer (August-September), and spatially over short distances (ca. 500 m) and small depth intervals (ca. 5 m) in an area without physical barriers. The magnitude of the seasonal variation was depth zone-specific, indicating that seasonal patterns from a given depth zone cannot be directly extrapolated to adjacent ones, let alone to a whole water body. In early summer, the adult fish displayed spawning aggregations, and their abundance was highest closest to the shoreline. In late summer, the adult fish were more evenly distributed and the assemblage was dominated by high abundances of juvenile fish. The results underline the importance of including several spatial and temporal scales into studies on fish distribution. The resulting patterns from such studies may appear idiosyncratic unless the nature and magnitude of seasonal variation and small-scale depth zone distribution are taken into account.