Resumo. Abstract Aim To compare abiotic variables and fish assemblage descriptors (species composition, richness, dominance and diversity) among coastal lagoons of the Tramandaí river system, southern Brazil. Methods Water and fish samples were taken monthly from April 2009 to March 2010 in the littoral zone of six coastal lagoons, three located at the north and three at the south of the Tramandai estuary. Thirteen environmental variables were measured. The fish assemblage samples were sampled with gillnets. We used multivariate analyses to investigate spatial variation in abiotic conditions and fish diversity. Results The samples at northern lagoons (Itapeva, Quadros and Malvas) were related to greater values of the turbidity and biochemical oxygen demand, while the southern lagoons (Fortaleza, Rondinha and Barros) were related to greater values of hardness, total dissolved solids, transparency, conductivity and salinity. The fish assemblages were similar in species composition. The species richness was higher in the southern lagoons when considering the same number of specimens. In the northern lagoons the assemblages were numerically dominated by Psalidodon aff. fasciatus and Loricariichthys anus and less diverse, while in southern lagoons were more equitable and diverse. Conclusions We concluded that the coastal lakes studied differ in the patterns of variation in abiotic parameters and this reflect in the water quality. Fish richness and species composition are similar, a likely result of the common and recent biogeographic origin of these lagoons. Fish assemblages in large and turbid lagoons present more dominance while the fish assemblages in small and clear lagoons are more diverse. These results may be useful for coastal management that prioritizes fish stocks or for proposing models of fish assemblages in subtropical coastal lagoons.