The river begins at
Joeperry Lake in
Bon Echo Provincial Park in
Addington Highlands,
Lennox and Addington County, northwest of
Cloyne, at an elevation of . It flows south, taking in the right tributary
Rainy Creek, and reaches
Pearson Lake. The river continues south and empties into
Skootamatta Lake at an elevation of . The right tributary
Killer Creek joins at the lake. It flows south over Skootamatta Dam, continues south and reaches Slave Lake at an elevation of . It continues south over a small dam, takes in the right tributary
Partridge Creek, and arrives in the community of
Flinton. The Skootamatta River then flows over Flinton Dam, heads southwest, passes into Hastings County and takes in the left tributary
Flinton Creek at an elevation of . The river continues south, takes in the left tributary
Little Skootamatta Creek at an elevation of , and turns west just north of
Highway 7. The river takes in the right tributary
Elzevir Creek, heads southwest under the highway at
Actinolite and runs parallel to
Highway 37. It reaches its mouth at the Moira River, at an elevation of , which flows into the
Bay of Quinte on Lake Ontario. ==History==