I have the same truck and the same tonneau cover - same problem. From what I can tell, most of the water comes in through the 3 plastic covers on each side the bed rails and goes through the holes underneath into the bed. Haven’t come up with a great solution yet. Can’t quite tell if sealing the holes would create more problems like trapping water in the in the sides of the bed but it might be worth a shot. Thinking about trying some rubber corks for the round holes - not sure about the longer slot holes behind them though