The Liangtan River basin is shared by Jiulongpo, Shaping a and Beibei district in Chongqing, China. The Liangtan River pilot project comprised identification of key pollution sources leading the Liangtan River basin pollution and the most efficient projects and technology for improving water quality in rapid urbanized area using the MIKE 11 modeling system. Ammonia-N (NH4-N) and chemical oxygen demand (COD) were found to be most illustrative representing nutrient load from municipal and diffuse rural sources and industrial sources, respectively. The scenario modelling for 2015 shows that in terms of improving the water quality, the different sectors should be addressed in the following order: Urban wastewater, industrial pollution load, rural wastewater, livestock pollution load, domestic solid waste and fertilizer pollution load. The largest improvements to water quality by 2015 can be achieved by enhancing municipal wastewater treatment to meet higher wastewater discharge standards for nutrients and by supporting investment in clean technology at the 50 largest industrial enterprises.