The Pirapama system in Pernambuco, Northeast Brazil, is one of the last major sources of adequate water supply in the state. A reservoir was constructed to store water for domestic, agricultural and industrial use. However, the formation of the reservoir pool flooded the marginal vegetation, starting an organic matter mineralization process, which resulted in eutrophication of the waters and depletion of dissolved oxygen concentrations, reaching anoxic conditions near the reservoir bed. This water body is also impacted by upstream inputs of domestic sewage, agricultural run-off and effluents from sugar-cane mills and distilleries. This work applied a one-dimensional vertical approach (CE-QUAL- R1) in order to simulate the formation of the reservoir pool, analysing the different operational alternatives. Eutrophication, anoxia and stratification potentials were studied. Water quality data obtained during 17 months are used to adjust the model rates and parameters. After model calibration-validation, hypothetical operational scenarios were simulated, taking into account different ways for water pumping (outtake elevations) and for discharging outflow excess (spillways or bottom outlet). Strong anoxic conditions (DO concentrations of less than 1.0 mg.L-1), associated to high eutrophication levels (high PO4 and Chlorophyll-a concentrations), were found in all simulated scenarios. Regarding water quality conditions in the reservoir, the use of bottom outlet for reservoir water releases presented better results than the other operational alternatives, since it makes possible releasing anoxic waters from the deepest layers of the reservoir pool. However, in these conditions, the water quality downstream from the reservoir was severely compromised.