The river begins at Stony Lake in the municipality of Douro-Dummer.

It passes the community of Warsaw, and takes in the right tributary May's Creek.

The river continues southwest into the municipality of Otonabee – South Monaghan, and passes under the Kawartha Lakes Railway and then under Ontario Highway 7.

The Indian River continues south, through the Hope Mill Conservation Area[4] and Lang Pioneer Village[5] at the community of Lang, flows through the community of Keene, and reaches its mouth at Rice Lake, which flows via the Trent River to Lake Ontario.

The Indian River drainage basin encompasses 210 square kilometres (81 sq mi) of land in two physiographic regions: the Peterborough Drumlin Field and Dummer Moraine.