This study illustrates the importance of sedimentation control on a global scale by introducing general concepts developed locally through field observations in eutrophic bay in Lake Biwa in Japan, and in Dongting Lake in China. The phosphorus concentration of suspended solids in water columns and in the bottom sediment during soil puddling before the transplanting of rice seedlings have been measured analytically. We have estimated the gross phosphorus loads and the economical loss of losing fertilizer from rice paddy fields in the whole Lake Biwa basin during the same period. Additionally, the discussions and conclusions made in the session ‘Ecosystem approach to water monitoring and management’ organized during the Third World Water Forum held in Kyoto, are introduced. The importance of sediment control in carrying out overall water quality programmes has been emphasized not only for watersheds with severe land degradation, but also for basins where the sedimentation impacts are considered rather small, and there is a need to reverse the long-term water quality trend in shallow reservoirs in international river basins, such as La Plata River basin in South America. Establishing international standards and regulations for controlling fine sediments, making an effective economic evaluation of the impacts induced by sedimentation applicable to local farmers, as well as developing an effective project focusing on treating sedimentation to improve nutrient control should be initiated on a global scale, as with the Global Environmental Facility project.