Resumo. Abstract Aim: Our study aimed at analyzing the diatom community structure of the plankton, periphyton, and surface sediments, and their relationship with the environmental variables of two reservoirs, Tanque Grande and Cabuçu, located in the city of Guarulhos, Metropolitan Region of São Paulo. Methods Three sampling stations were stablished in each reservoir. Samples of water and periphyton were collected during the dry (August 2013) and the rainy periods (January 2014), while the sediment was sampled only during the dry period. Water abiotic limnological variables were determined and quantitative and qualitative analyses were performed after the oxidation of diatom samples. Results Both reservoirs presented low values of electrical conductivity, pH and nutrients. The diatom community was represented by 30 taxa distributed in 20 genera. The diatom diversity was higher in the plankton, with three exclusive species. All taxa collected from the surface sediments also occurred in the plankton. The periphyton was represented by six taxa that were exclusive to this habitat. Conclusion Our results indicated that the environmental variables were responsible for the limnological changes in the two reservoirs. In the studied reservoirs, the species composition of diatoms differed slightly between the plankton and the surface sediments, while we found a different community in the periphyton, with the presence of exclusive species. The two climatic periods showed differences in the abundance of species, but no considerable differences in the species composition between the two reservoirs were observed.