Otonabee comes from the words ode which means "heart" and odemgat that comes from "boiling water".

After leaving the community to the Peterborough city limits, the river forms the border between Selwyn and the municipality of Douro–Dummer.

The river leaves Little Lake at Scotts Mills lock & dam, and heads south, passes under Ontario Highway 7, passes into the municipality of Otonabee–South Monaghan, and snakes its way without any other locks or dams to reach its mouth at Rice Lake, which flows via the Trent River to Lake Ontario.

[3] Some areas of Peterborough along the Otonabee are prone to flooding following heavy rains, such as happened on July 15, 2004 when 240 mm (7.3 in) fell in some locations in under twenty-four hours.

Both Susanna Moodie and Catharine Parr Traill lived on farms near Katchewanooka Lake.