The incident happened just before 3:00 Saturday afternoon in the river along the 200 block of Poplar Neck Road.
Officials say that the teenager was canoeing in the river when his vessel flipped over, catching him in between his overturned canoe and a rock.
It took more than two hours to free the boy.
He was taken to Reading Hospital for non-life threatening injuries. No word on his condition.
The incident remains under investigation.