According to the United States Census Bureau, the town has a total area of 8.3 square miles (21.5 km²), of which, 2.0 square miles (5.2 km²) of it is land and 6.3 square miles (16.3 km²) of it (76.02%) is water. However, according to the Town Government, Winthrop has a land area of just 1.6 square miles (4.1 km2).
Winthrop is connected by land skirting the Belle Isle Marsh Reservation, which is shared across the Belle Isle Inlet with East Boston. The town was originally separated from Deer Island. Although still an island by name, Deer Island has been connected to Winthrop since the former Shirley Gut channel, which once separated the island from the town, was filled in by the New England Hurricane of 1938. The town is considered the northern dividing line between Boston Harbor to its west and Massachusetts Bay to its east.
The town is divided into several neighborhoods with a central downtown area, including Court Park and Cottage Park along the Boston Harbor side of town, Point Shirley, Cottage Hill, Winthrop Beach, Ocean Spray and Winthrop Heights on the Massachusetts Bay side. The town is bordered by Revere to the north, and Boston on the northwest, west, and southeast. The water rights of the town extend to the edge of the county, and border those of Nahant in Essex County. As a result of the expansion of Logan International Airport, part of four of the runways (4L/22R, 4R/22L, 15R/33L and most of 15L/33R) lies within what was once the water rights of the town. By land, Winthrop is 5.5 miles (8.9 km) from Beacon Hill, the measuring point for all road signs in Massachusetts.