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The southern region of South America is arid and semi-arid, with an east-west gradient of precipitation. Most of its aquatic ecosystems are temporary lakes, with large variations in level and salinity. Although some ecological aspects of these lakes have been studied, the information on the relations between zooplankton and water chemistry, predation, effects of human activities, and the trophic status is scarce and scattered. The objective of this study was to determine the zooplanktonic composition, density, and biomass and their relationships with environmental variables in lakes of different phytogeographic regions of this region (Argentinian central pampa), subjected to different anthropic influences. Samples were taken from ten lakes with a salinity gradient between 0.38 and 115.5 g.L-1. The chemical composition revealed a distinction between sodic-bicarbonated and sodic-chlorinated lakes. We recorded 19 crustaceans and 30 rotifers and found inverse relationships between the richness and density and salinity and concentrations of most ions. Bicarbonated lakes were subsaline and characterized by greater richness and density, caused by rotifers. The most frequent species were Brachionus caudatus and Keratella tropica, and the crustaceans Bosmina huaronensis and Microcyclops anceps. The sodic-chlorinated lakes had lower richness and densities, and with distinguishable hyposaline and mesosaline populations with a predominance of neotropical endemic crustaceans, such as Moina eugeniae and Boeckella poopoensis, and hypersaline lakes with a predominance of Artemia permisilis. The biomass did not differ, but lakes with introduced fish fauna (subsaline and hyposaline) had smaller zooplankton, indicating the importance of the top down-effect in the zooplankton community structure.