Water accumulating in my spare tire compartment.

Check the trunk gasket, if it is bad in a certain spot then water may find a channel to run though, try looking for irregularities in the gasket, and take a couple buckets of water and throw on it to see if you cant diagnose it that way

I had a 1996 Neon and a 1997 Neon that had the same problem with water settling in the trunk. Each time it was a different problem. Even though these are obviously not the 2000 they might have a lot in common.

96 Neon
1) Remove the taillights and check the entire gasket area for proper seating. Run a small bead of RTV on the taillight gasket. Then reinstall the taillight. DO NOT GO CRAZY WITH THE RTV ! DO NOT OVER TIGHTEN. Dodge mechanics did this quite often to eliminate leaks when the taillight gaskets were suspect.

2) Remove the trunk liner and look at the seam sealer along each weld. Most likely if there is a leak on this seam you won't be able to see it. In order to completely stop the leaking I took clear RTV sealant and recoated the seam sealer. Yes you can use seam sealer if you have it around. Just recoat the seams all the way from the trunk floor to the taillights. You can't miss the line. This stopped the leak and the trunk has been dry for over a year now.

On the 1997 it was a lot harder to find, but this might help.

1) Same trick with the taillights. Just a little RTV on the taillight gasket then reinstall the taillight.

2) In the 95-99 Neon there were vents under the rear bumper cover where it met the quarter panels. The vent was rectangular and had breather flaps to allow air / moisture to escape from the trunk. In my case one of these vents had not been inserted properly into the quarter panel when the car was assembled. They just pushed into the holes in the side of the car and would click in. The tabs had broken off and the vent was hanging. (Again RTV to the rescue.) I glued each vent back into the quarter panels and put the bumper cover back on. I had the car for 5 years after that and never had another leak.

I know the 2000 isn't exactly like the 95-99, but there isn't really a whole lot of difference. You might find the same type of problems I had. Hope this helps.

I have a 2003 and I have the same problem there is no leaks anywhere and it only seems to be in the tire area, I was wondering if maybe it could be condensation, but then there is too much water for it just to be a little condensation.

My Neon did the same thing. I resealed the tail lights and replaced the trunk seal and it stopped. Hope this helps you