Hose it down thoroughly around the back of the car, let it drip dry for a few minutes before opening the tailgate and gradually pulling all the interior linings off. Look for a trace of water to follow all the way out to the faulty seal. Otherwise, the other source of water (if it's just accumulating in the spare wheel well and not dripping down from the tailgate) could be the common case of ingress through where the trailer wiring harness comes in through the floor near the spare wheel well. I've seen a few cars that have had water splash up there.