The current water quality status of the coastal Black Sea area is considered satisfactory, however there is a concern that this situation may reverse with the agricultural development of CEE countries. Point source emissions are relatively easily identified and dealt with, however diffuse sources especially from agriculture constitute over half of the remaining nutrient loads. The development of an indicator to be used as a benchmark of national nutrient management in respect to the environmental protection of the Danube River Basin would help with the fair application of mitigation measures for diffuse nutrient sources. This study developed a material flow analysis of nitrogen and phosphorus through agricultural activities for Germany, Hungary and Romania as examples. Nutrient balances were calculated for agriculture as a whole. The MONERIS model was used to estimate N & P loads to the Danube Corridor and into the Black Sea. The results of these analyses were then applied to various potential indicators. When the nutrient balances of agriculture as a whole was analysed, it emerged that Germany's larger production of meat and animal products which includes a large amount of milk led to more nutrient losses to surface waters compared to Hungary and Romania. Upon closer inspection, the more mineral fertilizers and feedstuffs that were imported, the more nutrient losses to surface waters accrued. A 'nutrient surplus' was identified and defined as the excess nutrients resulting from all inputs into agriculture minus agricultural products produced. Efficient nutrient management through the application of a 'ceiling' quantity of imported nutrients for feeding livestock so that the least amount of nutrients are lost to surface waters is therefore a possibility. This would curtail losses from developed countries such as Germany whilst allowing new member states such as Romania to develop and grow.