In semiarid regions is recurrent water depletion of some reservoirs during periods of prolonged drought, intensifying eutrophication. After water depletion events, new waters arrival and the trophic state improvement is expected. Therefore, the aim of this study was to evaluate the change of the trophic state after the reservoir’s drying due to a prolonged drought in the Brazilian semiarid region. It is expected that the trophic state improves after the water renewal by decreasing nutrient concentrations and algal biomass. This study was performed in a tropical, semiarid reservoir (Cruzeta Reservoir, Brazil), and was carried out during two different periods: 2012 (beginning of the prolonged drought) and 2019 (after the drying and reflooding). Analyses of Wilcoxon test and principal components analysis (PCA) were used to identify significant changes and patterns between the periods studied. The studied periods differed significantly (p < 0.05) with regard to maximum depth, pH, dissolved oxygen, conductivity, turbidity, inorganic and organic suspended solids, total phosphorus, soluble reactive phosphorus, nitrate and chlorophyll a. The hydrological regime of the Brazilian semi-arid region, governed by the prolonged drought period (from 2012 to 2019), contributed to significant changes in the volume and water quality in Cruzeta reservoir, increasing nutrients and algal biomass, intensifying the symptoms of eutrophication. Thus, contrary to the hypothesis of this study, despite the reflooding after the drought period, a worsening in the trophic state of the reservoir from eutrophic to hypereutrophic was observed.