The eastern section of the reserve is and encompasses
South Cape Beach State Park, Sage Lot Pond and Flat Pond. This eastern section offers a swimming beach that is a noted fishing site during the annual
bluefish and
striped bass migrations. It is also a sanctuary for protected species such as
piping plover and
least tern. Sage Lot and Flat Ponds are salt ponds to the east of the bay. The Quashnet River Property is in size. The
Quashnet River is the primary source of fresh water reaching the bay, which is mostly surrounded by upland forests. A three-mile (5 km) trail loops along the river. North Quashnet Woodlands is in size. These
pine woodlands encompass an abandoned
cranberry bog.
Trout Unlimited converted the cranberry bog channel into a river. Waquoit Bay is in size. Freshwater enters the Bay from four principal sources: the Quashnet/Moonakis River, Red Brook, Childs River, and groundwater overflow. The following rivers and bodies of water are salt ponds traced back to the east of the bay, reachable by
kayak: the Hamblin Pond, , Jehu Pond, Abigail's Brook The following freshwater ponds drain to the bay at the northern side and offer kayaking and fishing: Bog Pond, Bourne Pond, is just over in surface area and consequently is considered a Great Pond under the laws of the Massachusetts. It is kept in trust for all citizens and is not privately owned. Caleb Pond is in size. Childs River: Abandoned cranberry bogs and pine woodlands.
Washburn Island is a small nature reserve within the bay. During
World War II Washburn Island was used by the Army Amphibious Command as a landing area. This camp was home to the 594th Engineer boat and shore regiment. In the early 1960s Norwegian researcher Johannes Kr. Tornöe suggested Waquoit Bay as the location of
Leifsbudir ("Leif's booths or houses"), the long-sought site of the Norse colony of
Vinland. == Prominent fish and crustaceans ==