The enrichment of natural waters by nutrients from different sources has been associated with eutrophication in many Europe river basins. Materials accounting is a multidisciplinary approach to identify precisely the sources of pollution and to assess the most efficient preventive means to avoid these problems. A methodology for the evaluation of nitrogen balance was developed and applied for a case study on the Sava river basin, Slovenia. Total emission of nitrogen into the Sava river basin was estimated to be 18.6 kilotons per year. The results indicate that at present level of treatment and today's agricultural practice, the main sources of nitrogen originate from process wastewater management (62% from point sources and 4% from diffuse sources when compared to the total emission) and agriculture (3% from point sources and 28% from diffuse sources again compared to total emission). Atmospheric deposition contributes relatively in a small percentage of the total loading (3%). The results of the study showed that besides the reduction of point sources by implementing nutrient removal technologies, the management of agricultural pollution should become a major task with the aim to reduce the total load of nitrogen to river system.