According to the United States Census Bureau, the town has a total area of , of which is land and , or 11.17%, is water. Newbury lies just south of the mouth of the Merrimack River, and is drained by the Little River and Parker River, which, along with the Plum Island River, drain into Plum Island Sound, separating Plum Island from the mainland. Much of the town land is made of marshes, and is protected land, included in the Parker River National Wildlife Refuge, Old Town Hill Reservation Area, Kents Island Wildlife Management Area, Downfall Wildlife Management Area and parts of the Mill River Wildlife Management Area and Crane Pond Wildlife Management Area.