Same problem with bilge pumps. If your bilge thru hull is under the waterline you will get "back siphoning" of water entering once the pump stops.
A simple "flapper" scupper type valve is an easy install and cheap. These flappers once were standard on Bay 190's side scuppers and I use one over my bilge thru hull.
Maybe installing one in the baitwell will prevent backflow.
Maybe this will help,
Good Luck, Molar
