The Neponset River often fails to meet state bacterial water quality standards, except at the river mouth, where river water mixes with cleaner harbor water. Water quality does not consistently meet standards near Tenean Beach or MWRA's Commercial Point combined sewer overflow treatment facility outfall in Dorchester Bay.

Water quality problems in the Neponset watershed include bacterial contamination, eutrophication, and toxic chemicals in sediments. The lower Neponset receives contaminants from leaking septic systems and stormwater runoff.

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Neponset River Sampling Locations