[6] The area of the drainage basin of Bowmanville Creek is about 170 square kilometres (66 sq mi); almost all of the drainage basin is within Clarington, with the exception of a small part of the headwaters which are in the township municipality of Scugog to the north.

[5] Bowmanville Creek begins at the confluence of three unnamed streams near the settlement of Enfield at an elevation of 255 metres (837 ft).

It continues south into the community of Bowmanville, flows under Ontario Highway 401, takes in the left tributary Soper Creek, and reaches its mouth at Port Darlington on Lake Ontario at an elevation of 74.1 metres (243 ft).

About one kilometre north of Lake Ontario is the former Goodyear dam, originally built to provide electricity for a factory.

[9][10] A little further north, in what is now downtown Bowmanville, a dam provided water power for the Vanstone Mill until it was washed out in a storm in 1986.