I had this same issue last week. Water only came in while riding. My problem was that the 2 o-rings between the venturi and pump worked their way out of position. In my case the venturi was not tightened enough to the pump (need to fire my mechanic! i.e. oldest son) and the orings were pushed out and were mostly on the outside of the housing, but still held in place. Took it apart, got the o-rings in place, and everything was fine. I left the water in the hull to be sure the bailers were working and after a short ride, all the water had been pulled out.
Fun part was that I did all this on a neighbor's lift because it really was a 10 minute job, but would have been well over an hour if I had to go back to the ramp. Was afraid I would drop a bolt/nut/washer/oring the whole time.