It forms the principal headwater of the Ocklawaha River, a tributary of St. Johns River.
The source of the Palatlakaha River is at Lake Louisa, itself fed from the Green Swamp by two streams known as Big Creek and Little Creek.
From Lake Emma the river flows through a swampy area to enter Lake Harris.
The upper section of the river forms the 26 mile long Palatlakaha Run, a waterways trail for canoeists and kayakers organized by Lake County.
[2] There are 6 water level control dams on the river that are closed to keep water levels higher during drier periods.