Swimming, mountain biking, hunting, fishing, and car top boating are also permitted in some properties the trail passes through.

The northern terminus of the trail is also divided: its northernmost section ends at Plum Island in Newburyport, and a southerly branch extends to the sea in the town of Ipswich.

The middle third of the Bay Circuit passes through the towns of Walpole, Medfield, Sherborn, Ashland, Framingham, Southborough, Sudbury, Wayland, Lincoln, and Concord.

Features along this route include Noon Hill, Medfield Rhododendrons, the Charles River, Rocky Woods, Fork Factory Brook, Little Farm Pond, Broadmoor Wildlife Sanctuary,[3] Sherborn Town Forest, Rocky Narrows,[4] Ashland Town Forest, Sudbury Reservoir, Callahan State Park, Nobscot Conservation Land, Turenne Wildlife Habitat, Garden in the Woods, Devil's Den, Heard Farm, Great Meadows National Wildlife Refuge, the Mass Central Rail Trail—Wayside, Mount Misery (Lincoln, Massachusetts), Round Hill, and Haynes Meadow.

Features along this route include the Walden Pond State Reservation, Adams Woods, the DeCordova Museum, the Dana Museum, Flint's Pond conservation areas, Drumlin Farm,[5] the Bruce Freeman Rail Trail, Minuteman National Historical Park, the Assabet River, Fawn Lake, Nashoba Brook, the Sudbury River, Lowell National Historic Park, the Merrimack River, Kerouac Park, Lowell Heritage State Park, Carlisle Pines State Park, Middlesex Canal, Wilderness Park, the Concord River, the Minuteman Bikeway, Indian Springs, Deer Jump Reservation, Harold Rafton Reservation, Haggetts Pond, Indian Ridge Reservation, Harold Parker State Forest, Ward Reservation, Boxford State Forest, Bald Hill Reservation, Phillips Wildlife Sanctuary, Pomp's Pond, Georgetown-Rowley State Forest, Cleaveland Farms State Forest, Willowdale State Forest, Bradley Palmer State Park, Appleton Farms, Prospect Hill, the Ipswich River, Castle Neck River, Castle Hill, Castle Neck, the Ipswich Lighthouse, William Forward Wildlife Management Area, Parker River National Wildlife Refuge, Old Town Hill,[6] Joppa Flats Education Center,[7] and Plum Island.