On order to fix it, you must find the source of the leak. Dry the entire compartment thoroughly, then line the compartment with the diapers (as suggested by ducksface).
Drive a SHORT DISTANCE in the rain... then check the compartment. The idea is to catch the leak as it just starts, NOT after it has flooded the compartment.
You should see where it's coming in... then get to work replacing the door seal, aligning/adjusting the door, or sealing the place where the water is coming in.
You could start by just spraying the outside of the door with a hose for starters... you may find it.