The EPA maintains a long list of chemicals, some of which are considered toxic and others not. Toxic chemicals are monitored as they enter waterways due to runoff, dumping, and other sources like spills. The second link below details one example of how suburban New England waterways are monitored: by watching stormwater runoff, assessing the health of inland fisheries, and monitoring the nitrogen, phosphorus, and silicon loads in wetlands and lakes.
Various state, federal, university organizations actually do local monitoring of water quality. Those results are then submitted to the EPA for review. The EPA also compiles national statistics and reports for informational purposes. Data on various pollutants, pathogens, metals, and other chemicals is available as well.
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