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Lakes are sinks for incoming contaminants that recycle and maintain the impaired conditions. Lakes and their surrounding watersheds are unique and valuable ecosystems for both people and nature. Lakes are critical storage tanks for freshwater. Despite their importance, many of the world s lakes are in crisis. The main causes are inflow of domestic sewage, agricultural run-off, and discharge of industrial effluents, over-fishing, and introduction of exotic species and habitat degradation from population growth, expansion of cities. As more water is withdrawn for human use and more of it is returned to lakes and rivers badly polluted, there is less available to maintain vital freshwater ecosystems. Such activities have altered the physical, chemical and biological processes within aquatic ecosystems. These multiple threats have different histories, operate on different space-scales (catchment, local, regional and global) and involve different pathways of pollutant transfer (land, water, and atmosphere).