Check the seals around the tail lights, they can leak. Get in the trunk and close it and have a close friend (one that won't leave you in the trunk!) hose down the car to find the leak. Could be a split seal for the trunk lid too.
Also, I found that using a car cover keeps the majority of the water out of the car. Instead of lots of water in the trunk, a car cover will sluice off the majority and you'll end up with much less in the trunk until you fix it. Go buy a plastic container at the local grocery store for the wet cover when you put it in the trunk. I found one about 16" x 22" x 6" that works just fine to hold a wet car cover.
Also, I found that using a car cover keeps the majority of the water out of the car. Instead of lots of water in the trunk, a car cover will sluice off the majority and you'll end up with much less in the trunk until you fix it. Go buy a plastic container at the local grocery store for the wet cover when you put it in the trunk. I found one about 16" x 22" x 6" that works just fine to hold a wet car cover.