I face the same problem whenever it rains now or when the car is washed.
Recently, the rear passenger side foot area was soaked in 1-2 inches of water and the boot was terrible with more than half of the spare tyre drowned in water. I have a permanent polythene on the CD Changer in the boot and have to put the car cover on everyday.
I can see water droplets on the rear LHS door trim. My car is parked on an incline so as soon as it is brought down to stand straight, the water from the boot travels down to the passenger side rear seat and front seat carpet.
Please tell me what to check!