The distribution of species depends on the relationship with other species and the influence of abiotic factors, modulated by long‐term evolutionary and biogeographic processes. Polychaetes and fish are important components of the biota that inhabit estuarine systems, coexisting in various habitats, although the relationship between these groups and their responses to environmental variables is poorly understood. This study aimed to assess the concordance between fish and polychaete communities in three zones (inner, middle, and outer) of a tropical bay and to determine environmental influences on these communities. The raised hypothesis is that benthic fish is associated with polychaetes and that these taxonomic groups respond differently to environmental conditions. Environmental characteristics were the main drivers determining the occurrence of fish species and polychaetes families; however, no consistent relationship was observed between fish and polychaetes. Sediment granulometry seems to be an essential driver in determining polychaetes and fish distribution while turbidity and phosphorus were also important for fish. The three zones differed in both water physicochemical and sediment (nutrients and granulometry) variables, which determined their uses by different fish and polychaetes species. Only one fish species, the gerreid Eucinostomus argenteus showed a weak but significant association with the Goniadidae and Spionidae polychaetes, which may be associated with similar environmental preferences of both taxa. The lack of a consistent relationship between benthic fish and their likely invertebrate prey may be associated with the small spatial scale of this study and the early fish life stages. Most fish in shallow coastal areas are still in their early life, feeding mainly on polychaetes and other benthic macroinvertebrates, and as the area is shallow, planktonic organisms may be included in their diet, thus relieving predation pressure on benthic organisms. These findings are important to unveil relationships among different taxonomical groups and their environment.