I went to start my 2000 Jaguar S-Type last week and it wouldn't turn over. While looking for the fuel pump we opened the trunk, pulled up the cover and the whole thing was under about 2 feet of water (it completely covered the spare). We checked all the seals - nothing. the water has probably been there for more than a year. Never noticed.
Anyone ever hear of this problem? Know where the water would come from?
Got the fuel pump and relay changed and it is running now.

 

Usual problem is the rubber trunk/boot seal, you're describing exactly what happens.

 

is that the rubber around the trunk area (that you see when you open the trunk)?
we ran alot of water down the top of the car with the trunck open to see where the leak was but there wasn't anything - it all ran off.

 

there are about 12(3x4) holes in the center rear of the trunk floor covered with tar paper( you can see real well underneath the car). Punch them open with a screwdriver to allow any water that may get in to drain out in the future and forget trying to find how it gets in. We used to put seals on the trunk but the best thing you can do is open the drains that jaguar never thouht they needed to open. They did and even put in better duck bill style drains in later years