Lake Palakpakin is vulnerable to nutrient and sediment pollution, leading to eutrophication and siltation. Despite existing studies identifying the pollutants and detecting their concentration within the lake, their sources were generally attributed to agricultural activities, considered a nonpoint source. This research modelled the diffuse sediment and nutrient pollution affecting Lake Palakpakin, San Pablo City, Laguna using Soil and Water Analysis Tool (SWAT). This model is physically based, requiring DEM, soil map, LULC map, slope map, and meteorological data as inputs to model physical processes associated with water movement, sediment movement, nutrient cycling, etc. Due to the unsatisfactory statistical results of the calibrated model caused by insufficient hydrological data, the uncalibrated simulation was used. It revealed that the critical source areas for NO3-N and PO4 are found in agricultural lands and areas that are underlain by clay and clay loam. Critical source areas were also found along the stream connecting Palakpakin lake to Laguna de Bay. Meanwhile, higher sediment yields were distinct around Sampaloc Lake and the outlet of the other lakes and in agricultural and urban areas. Moreover, the model exhibited that an increase in precipitation coincides with an increase in sediment, NO3-N and PO4 loading.