Waste from aquaculture is considered as one of the possible causes of water quality deterioration in Manila Bay. Aquaculture in the area accounts for almost 30% of the total production in the Philippines. This high production entails intensified application of inputs that could possibly contribute to the nutrient (nitrogen, N and phosphorus, P) load in the bay. Thus, estimation of the N, P and SO4 loaded from aquaculture farms is necessary to develop more responsive intervention to reduce nutrient load in Manila Bay. Water samples were collected throughout the rearing period from different aquaculture systems in Cavite, Bulacan, Pampanga, and Bataan. The annual estimated N and P loaded from aquaculture farms were 12, 696.66 MT and 2, 363.01 MT, respectively. Fish pens/cages recorded the highest contribution accounting for 88% N and 86% P of the total load. It can be attributed to the direct release of uneaten feeds into the bodies of water. Roughly, 12% N and 14% P were obtained from the fishponds. Furthermore, the annual SO4 loaded from fishponds was estimated at 36,917.54 MT. Results of the study suggested that there should be an extensive monitoring of the environmental impacts and annual load of aquaculture farms for the sustainable regulations and management of aquaculture activities to reduce nutrient load and improve the aquaculture production as well. Finally, strict compliance to the regulatory guidelines and ordinances must be imposed to achieve the effluent quality standards.