Resumo. Abstract Zooplankton is an important community in aquatic ecosystems due to its linkage between primary producers and secondary consumers also playing a key role in cycling of organic materials. Aim: Therefore, our objective was to evaluate the effects of physicochemical variables of the water on the diversity of zooplankton community in seven tropical shallow lakes of Brazilian savannah. Methods Zooplankton samples were taken using a bucket and filtered 200 L by a 64 µm-mesh-plankton-net, and preserved for subsequent identification. Water temperature, dissolved oxygen, pH, electrical conductivity, turbidity, chlorophyll-a, ammonium, nitrate, nitrite, total phosphorus, and soluble reactive phosphorus were measured. Results The turbidity (decreases the temperature, luminosity and the system productivity) and ammonium (increases the toxicity) values were the major factors responsible for structuring the zooplankton community. On the other hand, also nitrogen and phosphorus (increase the productivity) are limiting in savannah lentic systems for the zooplankton. The higher α diversity was positively associated with aquatic macrophytes (increase of niches and refuge), whereas lakes with geographic proximity increase the similarity in species composition, decreasing the β diversity. Conclusions We conclude that the deterministic processes (niche theory), due to species have different ecological requirements, are different responses to environmental gradients and increase the diversity in heterogenic lentic systems.