It rises in northern Sussex County, approximately 3 miles (4.8 km) southwest of Milford, and flows generally east-northeastwardly, defining the boundary between Sussex and Kent counties; it passes through the center of Milford on its course to its mouth at Delaware Bay, 16 miles (26 km) northwest of Cape Henlopen.

[3][6] The lower 12 miles (19 km) of the river are considered by the U.S. Army Corps of Engineers to be navigable.

[7] A boardwalk known as the Mispillion Riverwalk follows the river in Milford.

As of 2003[update], an effort was underway to preserve a greenway along the river upstream and downstream of Milford.

[8] According to the Geographic Names Information System, the Mispillion River has also been known historically as:[1] "The first occurrence of this name (of the river) is in the form Mispening on a map of 1664, tentatively analyzed as meaning "as the great tuber (stream);" (Dunlap and Weslager, 1950)