The singer overhears a young woman lamenting her lover "gone over Chowan River." Her father had hired a captain to take her love away. The captain murdered her lover. Her father told her to take comfort and wait, but she drowns herself
The editors of Brown compare this to "Nancy of Yarmouth," but note that it is not the same song. In many ways it is better; it doesn't twist and turn as much.
The Chowan River has its headwaters in southern Virginia and flows into the North Carolina, meeting the sea in Albemarle Sound. But there is no localization beyond the mention of the river; one suspects British origin for the song (since it sounds like it involves a press gang). - RBW