The river is believed to have been named either for Robert Jones, an early European property owner in the region, or for "St. Jone", adapted from a Welsh spelling from St. John (Ioan).

[1] The St. Jones River flows for its entire length in east-central Kent County.

[7] From Silver Lake, the St. Jones River flows generally southeastwardly, along the east side of downtown Dover and past Legislative Hall, the Capital Square/Legislative Mall, and the Dover Air Force Base to Bowers, where it flows into Delaware Bay, approximately 0.5 miles (0.8 km) north of the mouth of the Murderkill River.

[8] The lower course of the river southeast of Dover is surrounded by brackish marshes and salt marshes, open water habitats, and wetlands.

A portion of the lower river, along with nearby Blackbird Creek, have received federal protection as the Delaware National Estuarine Research Reserve, part of the National Estuarine Research Reserve system.