Several species of endangered or threatened whales and turtles visit Massachusetts and Cape Cod bays, including right, humpback, finback, sei, and, rarely, blue whales. Also seen are the protected, but not endangered, minke whale, harbor porpoise, gray seal, harbor seal, and several species of dolphins.
During the 2008 surveys, 44 to 45 individual whales, one Atlantic white-sided dolphin, four harbor porpoises, ten humpback whales, five finback whales, four minke whales, and 12 to 13 unidentified whales were directly observed by the trained observers and other members of the monitoring team.

The total number of whales sighted was the highest since 2006, a year that saw increases after a period of relatively sparse sightings. Several whales were sighted in the vicinity of the outfall, 17 to 18 were within the Stellwagen Bank National Marine Sanctuary, and 18 were sighted in Cape Cod Bay. The Provincetown Center for Coastal Studies, which conducts systematic surveys of Cape Cod Bay, reported that twice the usual number of right whales visited the area in 2007 and 2008 as had been sighted during 1998–2006. The length of time that individual whales remained in or near Cape Cod Bay was also longer in 2007 and 2008 than had been typical in recent years.