Estuaries are highly dynamic ecosystems where fish communities respond to natural environmental variations and anthropogenic pressures. The Bahía Blanca Estuary is one of the most important coastal systems in the Southwestern Atlantic, although there is limited information on long-term changes in the composition of its fish assemblages. Our objective was to assess long-term changes in the fish species composition of the Bahía Blanca Estuary by comparing historical records from 1983 with recent surveys conducted between 2017 and 2025. These surveys combine commercial catch disembark samplings and scientific fishing operations. The fishing methods used by both the commercial fishermen are shrimp nets, channel closure nets and the scientific samplings used these same methods plus bottom trawling. Based on species presence–absence records, the comparison between the historical and recent periods showed an average Jaccard dissimilarity of 0.544, indicating a significant change in fish species composition. NMDS analysis revealed a separation between the historical and recent samples, although no clear temporal trend was observed in the recent period. Beta diversity partitioning indicated that species turnover explained most of the observed differences (βjac = 0.361; βjtu = 0.343; βjne = 0.018), representing approximately 95% of the total change. Seven species present in 1983 but absent in the recent period were recorded and six species were recorded only in the recent. A total of 23 species were present in both periods. The results show a reorganization of the fish species composition in the Bahía Blanca Estuary over the last four decades. The observed differences are mainly explained by species replacement rather than a net loss of species richness, suggesting changes in community structure rather than a progressive simplification of the assemblage. These findings provide a baseline for understanding long-term changes in the fish assemblages in the Bahía Blanca Estuary.