The shallow, brackish waters of the western Baltic Sea play a significant role in the life cycle of several commercial fishes, both as nursery and foraging areas. The fish assemblages of the inner 100 m is, however, surprisingly poorly studied, due to lack of effective methods for monitoring all fish species. In the present study, we applied Snorkel Visual Census (SVC) as a tool in monitoring shallow water (< 5 m) fish assemblages at two brackish shallow water localities in the Sound, Denmark. The survey was conducted through 15 consecutive months (June 2013-August 2014), during which a total of 36 species were registered. Assemblages were numerically dominated by Gobiusculus flavescens (Fabricius, 1779) (50%) and Gasterosteus aculeatus Linnaeus, 1758 (45%). Analysis of temporal, spatial and environmental factors revealed that temperature was the single most powerful factor affecting species richness, and had a significant effect on fish abundance, which in addition showed significant seasonal variations. Species richness showed a quadratic correlation to temperature with an optimum of ∼14°C. Abundances of individual species were affected by temperature and salinity, and showed both seasonal, spatial and diel variations. The negative effect of high temperatures on species richness was not seen at night, indicating that marine species utilize these areas as nocturnal feeding grounds or to avoid larger predators. Our findings show that SVC is effective in monitoring diversity of shallow, temperate water fish communities providing both qualitative and quantitative information on seasonal variations in species abundance and assemblage structure.