Wet cargo area

I noticed the other day that my cargo floor/ carpet was wet, any common problem areas known?
This is a 96 four door XJ with a roof rack without a sunroof.
Nothing obvious- no puddles, just the carpet gets wet...

Leaky hatch seals....

Either adjusy the latch pin closer in for a Better seal or replace the weatherstrip entirely....

Another thing to check is have you recently done anything that involved removing the tail lights? I had a leak in mine that was puzzling me and then happened to notice that when I put the tail light back in place I didn't get the bottom tab lined up leaving a gap for water to leak in through.

The carpet in my '96 kept getting wet, turned out my floor was swiss cheese. I hope you are more fortunate.

Possibly the roof rack. I have leaking at all 4 corners of the heep from the roof rack which in the rear runs down the pillars and drips just catching the floor and soaking the carpet.

the sealant that they use between the roof panells and the rear c pillar by the hatch at the drip rail where it wraps around the corner on mine cracked up. had huge cracks. Too much twisting on the trails.
ground it all out and got down to bare steel and then welded it all up. no more leaks from there.
the rear side 1/4 glass was also leaking. took it out and sealed it up. Fixed that.
The rear hatch glass also leaked. Tried to hide out under it when it was raining and eating luch, didn't work so well. It rained under the hatch. Again, out she came and sealed it up.
The radio antenna cable coming into the cab up front, the foam plug around it was leaking, some silicone fixed that up.
I had about 6 gallons of H2O in my jeep. those carpets act as great sponges!

I had problems with leaks where the floor rusted where my rear tire bracket was.

You could have holes in your floors. The insulation under the carpet holds water forever.

I just pulled out about 75 lbs of soggy wet insulation the other day. Nasty smelly discolored crap!!

Open the hatch all the way and look along the upper area of the rubber seal on the body, mostly towards the corners. Mine was clogged up with pine needles and such. When it rains, there's nowhere for it to go. It's supposed to follow the rubber around the corners and down to the bottom and out.