With the rapid development of aquaculture in lakes and reservoirs, its negative effects on water quality and aquatic organisms are clearly emerging. Toward a better understanding of these effects, chemical and biological monitoring was conducted in the Fangbian Reservoir to study the relationship between aquaculture and eutrophication. As a domestic water supply source, this reservoir has reached the mesotrophic level. The concentrations of total nitrogen (TN) and total phosphorus (TP) in the Fangbian Reservoir have frequently exceeded the prescriptive level according to the Environmental Quality Standards for Surface Water (GB3838-2002). Pond and fence aquaculture feeding is the main cause of high levels of nitrogen and phosphorus, accounting for nearly half of the total pollution, and causing the reservoir environmental capacity to be exceeded. The amounts of nitrogen and phosphorus that went directly to the reservoir through the residual bait and fish droppings in fence aquaculture were 42768 kg per year and 10856 kg per year respectively, from 2007 to 2009. About 2913 kg of nitrogen and 450 kg of phosphorus were imported to the reservoir through the exchange of water from the culturing ponds at the same time.Therefore, controlling the aquaculture scale and promoting eco-aquaculture are key measures for lessening the eutrophication degree and improving the water quality.