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The response of zooplankton assemblages to variations in the water quality of four man-made lakes, caused by eutrophication and siltation, was investigated by means of canonical correspondence analysis. Monte Carlo simulations using the CCA eigenvalues as test statistics revealed that changes in zooplankton species composition along the environmental gradients of trophic state and abiogenic turbidity were highly significant. Brachionus calyciflorus, Thermocyclops sp. and Argyrodiaptomus sp. were good indicators of eutrophic conditions, whereas B. dolabratus, Keratella tropica and Hexarthra mira were good indicators of high turbidity due to suspended sediments. Overall, our results showed that changes in the water quality of man-made lakes in a tropical semi-arid region have significant effects on the structure of zooplankton assemblages that can potentially affect the functioning of these ecosystems.