Resumo. Abstract Climate changes are predicted to strongly affect aquatic communities and consequences in coastal lakes and lagoons might be worsened by the tendency of salinization due to sea-level rise. Aim This study aims to evaluate potential fish community changes caused by a potential increase in salinity in a system formed by 41 interconnected lakes/lagoons. Methods We modeled the occurrence and abundance of 12 fish species under two scenarios of salinity change via marine water intrusion through the estuary of the Tramandaí river, in south Brazil, based on their contribution to β diversity. This was determined by the difference between the average number of recorded individuals and the salinity condition using ANOVA and Tukey's test, followed by generalized linear models with the estuarine connection projected for two future climate scenarios. In addition, we evaluated the effects of increased salinity on endemic species and the consequences of this environmental change on their endangered status. Results According to our results, salinity increases will lead to reductions in the distribution of freshwater fish species, which would become restricted to fewer lakes/lagoons (a 10 to 60% reduction in habitat area within the study region). These reductions in geographic distributions are even more concerning for the endemic species. Conclusions Our results demonstrate the need to assess vulnerability to climate change and that these criteria should be more clearly incorporated into species assessment protocols, such as those of the IUCN.