Resumo. Abstract Aim Relationships between species composition and variation patterns in diatom assemblages over six tropical reservoirs located in Southeast Brazil were explored. Methods Surface-sediment and phytoplankton diatom assemblages were determined and Canonical Correspondence Analysis was used to verify the set of environmental variables that best explain the species composition variation among sites. Results A total of 28 diatom taxa representing 20 genera were identified using light and scanning electron microscopy. Information on their ecological preferences was also provided. Humidophila biscutella is reported for the first time in Brazil whereas Sellaphora sassiana and Humidophila brekkaensis are reported for the first time in São Paulo State. Three groups of potential water quality indicators were delineated: the first suggests oligotrophic conditions, the second is related to cold waters with low luminosity in a mixing regime, and the third is a small group of tolerant species occurring in water with high conductivity, pH and total phosphorus conditions. Conclusion present study provided the first insight into the general diatom communities over six tropical reservoirs in Southeast Brazil and provided information on their ecology and distribution aiming bioassessment. The potential of water quality indicator diatom groups here outlined are in line with those reported in the literature and reinforce the importance of PEJU for the maintenance of ecological quality of reservoirs and reference conditions for the Metropolitan Region of São Paulo water sources.