Guys, check your spare tire well in the trunk...
 

So, yesterday I was troubleshooting a CEL I've been getting (P0496), so as I was testing the fuel tank pressure sensor, I accidently knocked a socket under the spare tire cover.

No biggy, I removed it, only to notice a ton of condensation over the jack and the plastic tub is sits in. Ok! So I remove it the tub.

Well, I found the condesation problem...

I had 4 inches of water in the spare wheel tub itself.

I have no idea how this water got there, or how long it had been there. Everything in the trunk itself was dry, no leaks, etc. We had some hard rain the night before, but how it got in there, I don't know.

So check yours.

Same thing happened to me about a month ago. I have an '04 that I purchased in the beginning of August this year. I was chasing down a rattle, pulled the spare tire and found the same thing, about 3" of water in the well. I wet vac'ed it out, dried everything then made an appt with the dealer. When I described the situation to the service manager he didn't seem to surprised. This is what read on my invoice:

Customer states that the spare tire was submerged in water.

Cause: Repair open body seam in trunk area
B5410 Reseal lower body seam in trunk areas
35 W94

Hope this helps, good luck!

I had mine repaired a while back. Basically they put caulking in the seam in the inside of the trunk. There has been no leaks since. I even had water leaking from the trunk underneath the rear seat.

Mine was full of water when I bought the car, but has never gotten another drop in there in 12K miles and 9 months of use. I sprayed the hell out of it and it's been in many rain storms with no leak. I can't figure out how it got in mine, but there are several common places on the newer model trunk. Do a search on the 2000-2005 forum and you'll find the lists of the many leak spot areas. I just can't make mine do it again, and I don't think it went away by itself.

Twice I have found water in my trunk as well. Never found where it came in though???

I found a leaking shock tower in my trunk. Take ff the plastic covers and take a look.

I sprayed some undercoating where the shock comes through from inside the rear wheelwells to seal them.

I don't have a GXP but I know that this trunk leak problem is a VERY common one that spans all of the 00-05 models. I've read that you can have certain spots sealed and it will clear it up, but that didn't seem to work for me.

I had about 3-4" of condensation in the spare tire well, which was ridiculous to me. I decided to have my mechanic friend drill 3 VERY small holes in the spare tire well and then he sealed the metal to prevent rusting. Fixed the problem completely! The car just takes a piss every so often, lol.

Re: Guys, check your spare tire well in the trunk...
 

I just got a P0496 EVAP code on the 04 bonneville SE today, I googled and came across this post, it's been raining here in the part of Texas I'm in, and sure enough, water in the spare tire well.

I found about 4" of water in my wheel well after purchasing my 04 with roughly 32,000 on it. I'm pretty sure it sat on the lot a while - I took the car to the dealer and they resealed a seam in the trunk ( not sure exactly where), replaced carpet & jack , but I've been keeping an eye on it and haven't seen water since.

Water in spare tire well
 

I have a 2001 Bonneville and had to use the spare and found 3-4" of water in the well. Does anyone know if a full size spare will fit in the well on this model and year?