This study explores a model depicting N (Nitrogen) and (P) Phosphorus contributions of the Philippines, Malaysia, and Indonesia in the Coral Triangle Large Marine Ecosystem (CTLME). N and P are the precursors to eutrophication and harmful algal blooms, and are threatening the health of the CTLME. The methodology used in this study is Substance Flow Analysis (SFA). Particularly, sub-systems in the areas of agriculture, aquaculture, and the activity "to nourish" are explored by a mass balance approach. The base year used is 2005. While the total contributions of the three investigated countries are estimated to be 700 kt/a of N and 190 kt/a of P, the study also deals with the contribution of each country and of selected sectors to the CTLME. The main sources of N and P are excess nutrients from commercial fertilizers in agriculture that accrue as stocks in soils and run-off to rivers; untreated human and animal wastes dumped in waterways; and effluents from aquaculture. A more prudent use of commercial fertilizers and interventions such as landfills and wastewater treatment plants are recommended to decrease the nutrient load in the CTLME. A knowledge-based body of work is necessary for decisions to save the Coral Triangle. The main result of this study is a consistent methodological approach for establishing the necessary knowledge base in the field of regional nutrient analysis. Additional work to collect better and improved data is needed to verify the conclusions about nutrient loads in the CTLME drawn in this thesis.