I just bought a 2001 323 protege and after some rain, found thewheel jack well in the trunkfull of water. Also about an inch in the spare tyre well, and a little in the well over the opposite side to the wheel jack. The back seat on the driver's side was wet, right at the back, and where the seat joins the back. But the carpet was completely dry and I didn't find moisture anywhere else. Does anyone have any idea where the water could be coming in?

 

A leaking seam somewhere? Top of a window, around the taillight(s)... Your guess is as good as mine. I'm guessing that the wheel wells might be taillight seals, but that is only a guess (Search and you will find other people mentioning leaking taillight seals, I know mine do...).

Z.

 

I had this same problem on my '92 323. Although they are different taillight designs, mine ended up being the seams where the taillight lenses attach to the assembly itself. First I tried sealing the taillights to the car better with silicone. That didn't do it. After it rains, turn your lights on at night and look to see if you have water inside of the taillight itself. If so, it could be the seams where the lenses meet the other plastic of the taillight assembly.