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I have 2002 3.0 S type and find even when the car is sitting on my drive in the rain, a small amount of rain water collects in the boot well between the spare wheel and the battery. I had the same problem with a 2,7 S type. I cannot see where the water is getting in - any ideas.
The most commonly quoted routes are the back light seals and the boot/trunk seal itself. For me, I believe it was the "v" where two panels meet under the trunk lid seal. Black mastic solved the problem on my car.
The first thing I did when I bought my 2001 S-Type 4.0 was to punch a hole in the boot floor next to battery in the lowest place in the 'ribs'.
When I worked at the dealer I saw MANY S-Types with water 'sloshing' in the boot floor so I made it a practice to punch a small hole near the battery to prevent the damage with the common leak for these models.
Jaguar issued a series of TSBs to address the ingress of water past the seals but a drain hole is a good 'fail-safe'.
I have recently just started getting a little water in the same spot just beside the battery. Remove the taillights everything looked perfectly fine. Today I found my problem I remove the black plastic centre cover from over the catch .
Just after taking the car out of the rain. This is what I found.
The water was entering through a locating peg For the rear bumper skin.