Benthos and zooplankton showed significant associations with the set of environmental variables (Monte Carlo test, p<0.05); however, the association was not significant for phytoplankton. Lake Chungara showed the greatest variation in composition and abundance of zooplankton between autumn-winter and spring-summer, while in the Huasco salar the physical and chemical characteristics were related to the composition and abundance of the benthonic fauna. Thus, changes in the water volume of these systems would have repercussions in chemical and physical variables, altering the species assemblage and possibly the efficiency and stability of ecosystem functions. (C) 2009 Elsevier GmbH. All rights reserved.