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The temporal phytoplankton biomass variation at two Neotropical reservoirs during an extreme drought season were analyzed. Here we sought to evaluate the main abiotic factors involved in dynamics of phytoplankton during this drought period. The main difference between the reservoirs was the intensive fish and shrimp farming in one of the reservoirs. For quantitative analysis, sampling with bottles were carried out at an average depth of 0.5m. Water temperature, pH and electrical conductivity parameters were measured in situ and water samples were collected for dissolved inorganic nitrogen and soluble reactive phosphorus analyses. Aquaculture was probably one among the causes for the reservoirs were so different in the physical and chemical variables, as shown by the principal components analysis. The results showed specific groups dominance in both reservoirs. In the Cachoeira II reservoir, an invasive dinoflagellate, Ceratium furcoides, was present in all analyzed months, while, in the Saco I reservoir, cyanobacteria group represented more than 50% of phytoplankton biomass, mainly Microcystis aeruginosa and Dolichospermum sp. In two reservoirs precipitation, soluble reactive phosphorus and electrical conductivity were positively related with phytoplankton. Phytoplankton biomass was considerably larger in the Cachoeira II reservoir, due to the greater size and biovolume of the dominant dinoflagellate. These findings suggest that species dominance in extreme drought events may be favored.