The Clare River begins at the junction of several unnamed creeks in the township of Stone Mills, Lennox and Addington County at an elevation of 189 metres (620 ft).

It flows southwest into Calpin Lake at an elevation of 171 metres (561 ft) at the community of McGuire Settlement, then continues southwest under Highway 41.

It then turns west and passes into the municipality of Tweed, Hastings County.

It takes in the left tributary Goose Creek and right tributary Otter Creek, flows past the settlement of Bogart, and empties into the east side of Stoco Lake on the Moira River at an elevation of 138 metres (453 ft).

The Moira River flows into the Bay of Quinte on Lake Ontario at Belleville.