Rivers in developing and emerging countries often lack good water quality. Tools to assess the water quality in rivers, including identification of possible sources of pollution, are therefore of increasing importance. The aim of this study is to apply mathematical material flow and spatial land use analyses to identify and geographically locate the main nitrogen and phosphorus sources and processes in Bang Pakong Basin (BPB). Potential measures to mitigate the nitrogen and phosphorus loads to the water system can then be efficiently evaluated. The combination of these two methods reveals the overall nutrient load as well as local "hot spots." This allows possible mitigation measures to be discussed with regard to their spatial location. This approach goes beyond previous work in which mathematical material flow analysis was shown to be a useful tool to investigate sources of nutrients regardless of their location. The results show that the main sources contributing nutrients to waterways are aquaculture, such as shrimp, tilapia, catfish, and sea bass farming, as well as rice paddies along the main river. Additional sources contributing nutrients to this basin are field crops, livestock, aquaculture, households, and industry. High levels of nutrient inflows come from feeds and fertilizers through aquaculture and rice cultivation. The excess nutrients run into the waterways by direct discharge from aquaculture and runoff processes from rice paddies. Scenario analysis shows that management practices for aquaculture, rice, pig, and poultry farming are key drivers for reducing nutrients in the BPB.