The St. Marys River rises as a tiny stream flowing from the western edge of Trail Ridge, the geological relic of a barrier island/dune system, and into the southeastern Okefenokee Swamp.

Arching to the northwest, it loses its channel within the swamp, then turns back to the southwest and reforms a stream, at which point it becomes the St. Marys River.

It then flows south, then east, then north, then east-southeast intersecting I-95 near Yulee, and finally emptying its waters into the Atlantic, near St. Marys, Georgia and Fernandina Beach, Florida.

[10][11] On 6 July 1805, Lieutenant Robert Pigot of HMS Cambrian arrived off the harbour in the French privateer schooner Matilda, which the British had captured three days earlier.

On 7 July Pigot took Matilda twelve miles (nineteen kilometres) up the St Marys River to attack three vessels reported to be there.