During the last decades, limnological studies on Chilean systems have contributed to know the species composition and main environmental variables of many water bodies distributed over a wide latitudinal interval, from 18º to 53º S. However, we still lack of a comprehensive view about the structure and functioning of regional freshwaters. In this work we review the available information about pelagic biota from Chilean basins, in order to reveal patterns of species distribution and their possible association with environmental variables. We built presence-absence matrices for phytoplankton, zooplankton and fish over lakes and basins. From this database, we performed parsimony analysis of endemicity as a tool for determining fundamental distribution patterns of freshwater biota. Also, we assessed the relationship between species occurrences and some available site-related variables. Our results indicated that latitude exerted the strongest influence on species distribution, although altitude, longitude, and area also exerted significant effects for some groups. On the other hand, our results suggest a relationship between the degree of vagility of the groups and the degree of metacommunity structuring, related to the number of endemicity areas.