 According to the United States Census Bureau, the city had a total area of 0.968 square miles (2.507 km2), including 0.929 square miles (2.407 km2) of land and 0.039 square miles (0.1 km2) of water (3.99%),

The City of Bordentown is surrounded on three sides by Bordentown Township and on the western side by the juncture of the Delaware River and Crosswicks Creek, which is the border with Hamilton Township in Mercer County.It is bounded on the east by U.S. Route 130 and U.S. Route 206, on the south by Black's Creek and Interstate 295, and on the north by the Mile Hollow Run.Across the Delaware River is Falls Township in Bucks County, Pennsylvania.