Coastal lagoons are inland water bodies connected to the sea and influenced by freshwater discharge, so these environments undergo constant changes in physical–chemical water characteristics. Transitional environments are important for promoting breeding, refuge, and food areas, besides serving as possible nursery habitats for fish species. In the present study, we analyzed the structure of the fish assemblages in a shallow marginal area of Mirim Lagoon, which belongs to the Laguna Estuarine System (LES), by seasonally evaluating the composition, structure, and diversity of the assemblages. Fieldwork was carried out between September 2017 and August 2018 with three monthly replicates using a beach seine net. Analyses were conducted to highlight the general patterns of the assemblages and to verify seasonal variations in composition, abundance, and diversity. The common species were defined using a species abundance curve, while the seasonal variation in diversity was evaluated using integrated rarefaction and extrapolation curves that correspond to the three orders of Hill numbers. The differences in the specific seasonal composition were indicated by dbRDA and the existence of statistical differences was tested using a PERMANOVA. In total, 3,556 individuals distributed in 16 families and 26 species were caught, with the predominance of Atherinella brasiliensis, Eucinostomus melanopterus, Coptodon rendalli, Eucinostomus argenteus, Mugi lliza, Anchoa tricolor, and Achirus lineatus that represented approximately 98% of the total. Regarding seasonality, the highest abundance was caught in the winter, while the lowest abundance was caught in autumn. The PERMANOVA indicated differences between spring and autumn and between autumn and winter. The main differences between these seasons are associated with the number of individuals caught, species abundance, and species composition. The presence of juveniles of several fish species, especially non-resident species, demonstrates the importance of the shallow area of Mirim Lagoon as a breeding, growth, and protection site that serves as a possible nursery habitat for these species.