The freshwater resources of Asia are under enormous pressure given the high and increasing population densities of the region, and the serious degradation of many lakes and rivers due to agricultural, industrial and urban development. Global climate change is likely to exacerbate these pressures through changes in the hydrological balance; influences on stratification, algal blooms and deep water re-oxygenation; and for high altitude sites such as lakes on the Mongolian Plateau, accelerated permafrost melting and desertification. Eutrophication and other processes of water quality degradation are especially severe in many parts of China. At Lake Taihu, a drinking water supply for 40 million people in central China, toxic cyanobacterial blooms now occur throughout the year. In the Province of Yunnan, many of the shallow lake waters are highly polluted and are of human health concern. Lake Biwa, Japan's largest freshwater body, has experienced many environmental problems over the last 50 years including loss of species habitat, changes in oxygen content, and blooms of noxious cyanobacteria. Two multi-disciplinary research programs involving specialists in hydrodynamics, bio-optics, biogeochemistry and freshwater ecology have generated new insights into the structure and functioning of the Lake Biwa ecosystem, and have contributed an improved and lakes elsewhere, will especially depend on an improved scientific understanding of the Iimnological controls on water quality. It will also be fostered by cross-disciplinary and international exchanges of information, and a commitment by scientists, residents and others with a vested interest in water quality, including regulatory authorities, to work together towards the common goal of long term, integrated protection of the lake and its surrounding watershed.