My 2000 was in at least 6 times when it was new. It turns out there are four areas where it can leak:
-spoiler bolts not sealed
-tail light gasket
-seam not sealed
-trunk gasket
The dealer tried the first 3 several times before they kept the car for a week and finally replaced the trunk gasket. Voila. Dry trunk ever since.

I had a similar issue with my 01. In the winter of 02 we had a couple "O" days of down pours. My 01 sits in my drive at a step incline (nose up). After the first heavy down pour I ended up with about 14 inches of water in my left rear passenger floor. Took it to the dealer 4 times to get it fixed. Finally on the forth try they got it right, they had it for 2 weeks. It really was bad and I was getting really pissed!

My wife just complained about this yesterday, (we had a downpour here in St Louis) . This is good info and I'll be taking a look. Out of the 4 listed is there a most likely culprit?
BTW what does CHMSL stand for?

center high mounted stop lamp , 3rd brake light for those of us on earth

Just want to chime in. I live in a very rainy climate. When I open the trunk after a very heavy extended rain, as noted, a lot of water pours out from the trunk latch. The car was back to the dealer at least 3 times. There must be 20 pounds of sealant in the trunk!! Really. Nothing has helped. It has been there since day1. I'll have to try some of the remedies noted here.

I know the dealer told me that water leaks are among the most difficult problems to troubleshoot.

I couldn't get the leaks in my '00 Bonney to stop, so I pulled the rubber plugs from the bottom edge of the trunk lid, closest to the bumper when closed. Water drained from there, presto, no more leaks. Of course, it may rust out in 15 years, but I already traded it in on a 2002, which did the same thing the first week I had it, so pulled those plugs, too, with good results. Just waiting for rust...

I found a very small fold in the gasket on the third brake light. I put a bead of clear silicone on it. That was weeks ago. We've had buckets of rain since. It is fixed. Thanks Guys!

I fixed mine a couple months back after checking all the causes listed here, I found another cause to add.
Bent seal lip along the bottom edge of the trunk.

I tore out all the coverings and climbed in the trunk with a flashlight while my kid hosed down the area. It was coming in along the seal at the bottom corner on the driver’* side. Pulled the seal off, took a pair of channel locks and bent the metal edge up. Fixed now.
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hey thanks for all the diagrams, makes it so much easier to look for my own leaks

I was getting water in my trunk. It would pool down around my spare tire. I solved the problem by removing the two plugs located on the trunk lid tip and haven't had any problems since.....

Mind you, it may not solve the problem, but it kept the inside dry.