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Droughts are large-scale perturbations that affect freshwater ecosystems worldwide. A water level reduction caused by drought is an important driving factor of phytoplankton dynamics. It has been suggested that a water level reduction alters the light and mixing regime and increases nutrient concentrations and phytoplankton biomass favoring cyanobacterial blooms. We took advantage of two exceptionally dry years in the Brazilian semi-arid region to investigate the effects of the water level reduction on the water quality and phytoplankton communities of two shallow man-made lakes. In both lakes, the water level was reduced by half, while the water turbidity, conductivity, and nutrient concentrations increased. In the deeper lake, the phytoplankton biomass increased and was dominated by a cyanobacteria group as expected, but it decreased in the shallower lake and was dominated by mixotrophic flagellate groups. This was because of sediment resuspension by wind and fish facilitated by a water level reduction and increased the water turbidity more strongly in the shallower than in the deeper lake. Therefore, a water level reduction caused by a drought may either increase or decrease the phytoplankton biomass and cyanobacteria dominance in tropical shallow lakes depending on the lake depth and the concentration of inorganic suspended sediments.