The macrozoobenthic diversity patterns along a brackish-freshwater salinity gradient have been identified, considering effects of differences in the level of hydrological connection of coastal lakes with the sea on the structure of benthic invertebrate communities. The study is based on samples from six coastal lakes located along the southern coast of the Baltic Sea in Poland. The analysis of environmental and biological data confirmed the existence of stable phases (brackish water vs. freshwater), but as a result of periodical intrusion of seawater, adaptation of animal communities takes place, which was reflected in low values of the predictors describing them (number of taxa, density and diversity). Redundancy analysis indicates that values of conductivity and salinity are the major factors that determine the abundance of dominant groups of benthic fauna. The gradient of hydrological connection of the lakes with the sea accounted for 50% of the variance in biological data, physico-chemical variables for 25%, trophic variables for 15%, and only 9% of the variance was unexplained. The major implication of our results is that coastal lakes that differ only slightly in salinity can have alternative, regional patterns of diversity of structure of benthic fauna. Periodical inflow of brackish waters initiates adaptive cycles of benthic fauna, and their frequency is strongly linked with the hydrological regime. The rhythm of the inflow of seawater is variable, so that management and protection of coastal lakes are extremely complicated.