Investigation of physical profiles of nutrients within socio-economic systems is one of the key approaches to cure eutrophication. Applying a substance flow analysis (SFA) method for the case of Dianchi basin located in southwest of China, we established a regional static SFA model (PHOSFAD) in 2000 via balancing societal phosphorus flows. Aggregate characteristics of the overall phosphorus throughput, and physical efficiencies in relation to phosphorus uses of production and consumption sectors, including mining, processing, farming, livestock husbandry and household consumption, were subsequently identified. The methodology and results of this study illustrate applicability and value for rational decision-making aiming to curb eutrophication of Dianchi Lake.