It flows generally eastwards for approximately 20 miles (32 km),[3] forming the boundary between Marion and Putnam Counties, before draining into the Ocklawaha River near Orange Springs.

[4] The creek's outflow enters the Oklawaha near Orange Ferry, along the stretch of river where the Ocklawaha is impounded to form Rodman Reservoir, part of the abandoned Cross Florida Barge Canal; the creek was considered to be a significant source of water for the reservoir, providing a 20-year mean discharge of 188 cubic feet per second (5.3 m3/s) as of 1973.

The St. Johns River Water Management District includes this area in the Orange Creek basin.

[10] A number of springs and small streams in Alachua County flow into Paynes Prairie, into other sinkholes, or into swamps that have no surface outlet.

[14][15] A dam impounds Orange Lake at its exit into the creek; it was the source of controversy in the late 1980s with some calling for its removal.