Climate change is affecting the global hydrological cycle and is causing drastic changes in the freshwater hydrological regime. Water level (WL) reduction caused by drought tends to increase the concentration of nutrients favoring the dominance of cyanobacteria. We hypothesized that the WL reduction favors the dominance of cyanobacteria at regular dry conditions, but at extremely dry events mixotrophic algae would thrive because of light limitation due to increased resuspension of sediments on the water column. To test our hypothesis, we compared phytoplankton traits and water quality variables between two sets of reservoirs located in two watersheds with contrasting precipitation regimes within the Brazilian semi-arid. The reservoirs were compared in a dry period and in an extremely dry period to evaluate the response of the variables to an extreme drought. Drought intensification decreased the reservoirs’ WL and water transparency and increased the total phosphorous. Cyanobacteria dominated in the dry period, and the contribution of mixotrophic algae increased in the extremely dry period. Thus, phytoplankton with mixotrophic potential was favored by the extreme drought. This result suggests that this can be one possible scenario for phytoplankton communities in reservoirs of semi-arid regions if extreme droughts become more frequent because of climate change.