Rain, onshore winds, and tides all affect beach water quality. Bacteria counts can increase with more rainfall, resulting in stormwater discharges and, occasionally, combined sewer overflows in larger rain storms. Swimming in Boston Harbor is not recommended for 24 hours after any heavy rain storm.

The Massachusetts Water Resources Authority and the Department of Conservation and Recreation (DCR) test the water quality at all of the beaches along Boston Harbor weekly, and test five beaches daily in summer. Beaches in Boston Harbor are managed by DCR , which posts red flags at beaches when they have poor bacterial water quality. This information is available in summer from DCR's Beach Water Quality Hotline at 617-626-4972. In addition, daily beach water quality data is made available online by the Massachusetts Department of Public Health.