Inside your trunk, there should be over 6 or so small black rubber plugs... over time they dry rot, and with the right amount of pressure from water from ur wheels splashin up, they will fall out, or begin to leak. One thing I did to solve this was use gorillia glue the plugs back in. this last longer. I also used JB Weld on one where a plug had been lost. Also I used a peice of strong blue latex glove with gorillia glue as a temporary seal that has last for over a year. So you can be pretty creative to solve this problem... pretty much its just that rubber seal... if you can replace them more power to you. but to be honest I would prefer feeling them in... if you have any bondo around you can always dab a little bit in and sand it some what smooth, don't have to be to smooth as I assume it will be covered up, and if not, then obviously you don't care if ur trunk looks a little ghetto... I'm not sure how well the bondo would hold but I would think it would work.
If you decide to use JB weld... it tends to fall out of the hole before it drys... so u have to use something to hold it in place until it dries