Binghamton is located at 42°6′8?N, 75°54′42?W (42.102225, -75.911797)GR1.According to the United States Census Bureau, the city has a total area of 28.6 km² (11.0 mi²). 27.0 km² (10.4 mi²) of it is land and 1.6 km² (0.6 mi²) of it is water. The total area is 5.43% water.

The north branch Susquehanna River passes through downtown Binghamton. This branch rises in eastern New York and receives a number of tributaries above Binghamton, most notably the Chenango, which joins from the north just outside of the business district. Major floods occurred in the city during 1865 and 1936.

In 1935 the Chenango suffered a flash flood, which was damaging, but less severe once it joined the larger Susquehenna. So much water came from the Chenango, that the Susquehanna flowed backwards for some distance above the confluence. In 1972 the remnants of Hurricane Agnes flooded the entire Susquehanna basin downstream from Binghamton, but the damage in the city was minor.