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.