Global biogeochemical cycles have been deeply modified by human activities in recent decades. But detailed studies analyzing the influence of current economic and social organizations on global biogeochemical cycles within a system perspective are still required. Country level offers a relevant scale for assessing nutrient management and identifying key driving forces and possible leaks in the nutrient cycle. Conceptual modeling helps to quantify nutrient flows within the country and we developed such an approach for France. France is a typical Western European country with intensive agriculture, trade and an affluent diet, all of which may increase internal and external P flows. Phosphorus (P) was taken as a case study because phosphate rock is a non-renewable resource which future availability is becoming increasingly bleak. A conceptual model of major P flows at the country scale was designed. France was divided into agriculture, industry, domestic, import and export sectors, and each of these sectors was further divided into compartments. A total of 25 internal and eight external P flows were identified and quantified on a yearly basis for a period of 16 years (from 1990 to 2006) in order to understand long-term P flows. All the P flows were quantified using the substance flow analysis principle. The results showed that the industrial sector remained the largest contributor to P flows in France, followed by the agriculture and domestic sectors. Soil P balance was positive. However, a positive P balance of 18 kg P ha−1 in 1990 was reduced to 4 kg P ha−1 in 2006, mainly due to the reduced application of inorganic P fertilizer. The overall country scale P balance was positive, whereas half of this additional P was lost to the environment mainly through the landfilling of municipal and industrial waste, disposal of treated wastewater from which P was partially removed, and P losses from agricultural soils though erosion and leaching. Consequences for global P resources and soil and water compartments are discussed. Some opportunities to more effectively close the P cycle in France by both improving the intensity of P recycling and decreasing losses are quantified.