Appreciate what has worked for others, this is my experience:
About two months ago, I noticed a musty odor in the trunk of my 95 LX. Remembering this thread I had read on tccoa.com, I checked it out to find a couple inches or rusty water in the spare tire well. I had my car in my one-car garage working other issues from late December through January, and it looked like the water had been in there at least that long. So I'm left wondering where did the water come from. In addition to the car being outside from last summer through December, occasionally I run a sprinkler under the car during the winter/spring to wash off the salt from underneath. So I was racking my brain about where could the water have come from.
The donut spare although rust on the wheel appears to still be usable. Pumped it up to the recommended 60 PSI. I heavily oiled up and worked the jack and it also appears to still be usable. Pulled the floor covering out of the luggage compartment (trunk) and cleaned the rust stains off of that. Pulled out the lower cushion of the back seat, no water found there.
Starting off with a dry trunk, I lined it with kraft paper, thinking it would allow me to see the source of a leak. Then washed the car and ran the sprinkler underneath it. No water found in the trunk. Then with the trunk lid open I ran the hose on the area around the trunk outside of the weatherstripping, no water leaking into the trunk. Still not finding the source of the leak.
Last week I did a thousand miles of highway driving, mostly in the rain. The Washington to Boston 500 and back. It poured while I was there. No water in the trunk.
After I got home, I reinstalled the luggage compartment floor cover and plastic piece that attaches to the rear of the luggage compartment. After I installed it, I noticed that the plastic piece was overlapping the trunk weatherstripping. Speculated that that could cause water to leak into the trunk. I fixed that, pulled the weatherstripping so it was outside of the plastic piece that runs the width of the rear of the luggage compartment.
I'm concluding that the reason for the trunk of my car collecting water in the spare compartment is because either the trunk weatherstripping wasn't properly sealing around the rear trunk plate, or maybe, I left the car out in the rain with the trunk lid not closed tightly and rain got in. In any event, on my '95 LX, I think the problem was because of an insufficient seal of the trunk weatherstripping. I think the water leaked in when it rolled down the trunk lid around the weatherstripping until it fell into the trunk through an untight seal at the bottom. If in the future I find otherwise I'll provide an update on this site as needed.
Good luck finding the source of any leaks if you have this problem.