Water quality tools are necessary to control and prevent eutrophication in reservoirs, particularly reservoirs with aquaculture cages because these lead to nutrient loads from fish food. A combined bioenergetic and water quality model was implemented in this study to assess the contribution of aquaculture activity to algal growth in El Pañe Reservoir, Peru. In addition to its complexity, four different algal groups (Chlorophyta, Cyanobacteria, Chrysophyta, and Cryptophyta) were modeled according to their dominance in the water column of El Pañe Reservoir. Moderately reasonable distribution plots of chlorophyll-a were obtained when calibrating the model despite data scarcity and low R2 values (0.04 in the intermediate zone and 0.16 in the dam zone of the reservoir). Six scenarios of annual aquaculture production were analyzed, and the scenario with an annual fish production of 100 000 kg increased Cyanobacteria blooms to a dangerous level. Furthermore, the results indicate that an annual aquaculture production of 36 000 kg still requires careful consideration in terms of its impact on the water quality of El Pañe Reservoir.