Despite increased attention to the need for sustainable agriculture, fertilizer application rates above crop requirements remain common agricultural practices in South Korea, causing eutrophication of freshwater and coastal ecosystems. The aim of this study is to quantify phosphorus (P) inputs, outputs, and retention in a forested-agricultural watershed. The P budget showed that the combined use of chemical fertilizer and organic compost was the largest source of P (97.6% of the total) followed by atmospheric wet deposition (2.1% of the total P), whereas forest export (0.2% of the total) and sewage treatment plants (STPs) (0.1% of the total) were negligible. The P outputs were crop harvesting and hydrologic export to surface water. The P balance showed that P inputs are higher than the P outputs; approximately 87% of the total P input was retained in the soils within the watershed. However, P concentrations in drainage water were still high enough to cause eutrophication of downstream reservoirs. The results provide important details on the proportion of P export and retention in the watershed. This will help efforts to improve water quality and design better management strategies for agricultural nonpoint source pollution.