Within watershed ecosystems, water purification is one of the numerous ecological services provided to the surrounding environment and population. Through the purification process provided by the watershed, metals, viruses, oils, excess nutrients, and sediment are removed from the water as it filter through the system, providing clean water for drinking, industrial purpose and general recreation. As the water flows through compacted soil, surrounding wetlands and riparian forests, microorganisms and the biological composition of the wetlands reduces significant levels of particulate concentrations. Wetlands typically remove 20 to 60 percent of metals, retain 80 to 90 percent of sediments, and 70 to 90 percent of nitrogen. Forests further reduce nitrogen levels by up to 90 percent and phosphorus levels by 50 percent, while also protecting the loss of topsoil and reducing erosion. 
Changes to the natural landscape, such as paved surfaces, altered waterways, loss of forested area and the introduction of non-native species reduce the effectiveness of these ecological services provided by wetlands. Paved roads increase the rate and intensity of runoff and diverted waterways, mostly used for agriculture alter the effectiveness and general flow of the entire ecological process. When introduced, invasive species may deplete native populations which contribute to the degradation and overall weakening of ecological services.
Other watersheds both within the continental United States and other continents, provide similar services and are effected by many of the same ecological stresses. The Belgrade Lakes in Maine, currently are experiencing problems with introduced invasive species, in particular, Eurasian water-milfoil. This invasive plant, speculated to have been introduced to the ecosystem from boats, outcompetes native vegetation and stifles the overall biological productivity and biodiversity of the water body. 
Within the Maryland and Virginia area, the Chesapeake has been widely affected by runoff and nitrification from the surrounding population. Primarily the result of unchecked agricultural practices, the composition of the bay has been widely altered with the introduction of numerous fertilizers such as phosphorus and nitrogen, which have dramatically reduced native populations, such as clams, which act as a filtering mechanism for the overall watershed.
Some of the most prevalent issues to the Champlain Basin, are high levels of phosphorus and toxic substances. In 1993 a join water quality agreement was signed between the States of New York, Vermont and Quebec, which established management plans to reduce phosphorus concentrations as measured in the sediment. New York and Vermont specifically examined point and nonpoint sources of phosphorus runoff, and estimated that the annual phosphorus load to the Lake needs to be further reduced by 57 metric tons (relative to 1995 levels). In order to achieve this reduction, stricter regulations, on agricultural and other industrial externalities should be developed to reduce their negative effects.
The protection and restoration of wetlands also should be widely considered as one of the most effective means to increase ecosystem service functionality. Measures which would restrict the unsustainable use of lands which contribute to these services could include building permit restrictions, limited public access and punitive measures for imposed externalities would all greatly benefit the general watershed and its inherent natural abilities. Furthermore, maintaining the natural structure and composition of waterways and wetlands dramatically improves their ability to mitigate the effects and intensity of natural disasters such as floods.