Here, we aim to test for differences in salinity and thermal tolerance, species traits and distribution patterns among the three divisions using data for about 21,000 species. We found that primary fishes have much less salinity tolerance than secondary and peripheral species, with some secondary fishes displaying the highest tolerances (>100 ppt). We also provide, for the first time, evidence of significant phylogenetic signal of salinity tolerance, comparable in magnitude to conservative traits, and show that studied peripheral and secondary species have maintained or even developed salinity tolerance, in contrast to primary fishes. Although peripheral fishes are the most different, and despite the large variability observed within some families, primary and secondary species also show differences in morphology and life-history traits. The distribution ranges and genetic diversity of primary and secondary fish divisions are similar and differ from peripheral species, suggesting that although there is evidence of oceanic dispersal of a few secondary fishes at evolutionary time scales, it is a rare contemporary phenomenon. Importantly, a few findings outlined in this study, namely, differences in salinity tolerance, rely on limited data. Thus, we urge for additional empirical research on the salinity tolerance of freshwater fish, which remains largely unexplored, to help clarify differences among and within clades.