Water quality models are important tools for facilitating assessment of the main processes occurring in an aquatic system. To this end, a water quality analysis simulation programme (WASP8) was used to assess the eutrophication process in El Pañe Reservoir. The reservoir has a useful water volume of 99.6 hm3 and is connected to six other reservoirs located in the Chili Basin of the Arequipa Region. El Pañe Reservoir, which is the basin head, has exhibited eutrophication problems since 2014, causing water treatment problems for human consumption and a high probability of cyanotoxin releases from intensive algal blooms. Accordingly, the reservoir was divided into 11 segments, ammonia, nitrate, phosphate, total phosphate, dissolved oxygen, water temperature and chlorophyll-a being the simulated water quality parameters. The simulations were set in a steady state condition for 3 years from October 2015 to October 2018, subsequently determining aquaculture activity and benthic flux as being meaningful nutrient sources impacting the phytoplankton community. The results of the present study provide necessary evidence of the need to exhaustively quantify both sources in future research, which will aid decision makers in identifying the best management option that can help guarantee the sustainable development of the involved human activities.