If you have any rust around your rear wheel-wells, there could be a hole from the wheel well to the truck. I pulled back the carpet in my trunk and found a huge hole where the wheel-well and the car's side panel connects. There would most likely be a lot of water in there if this were the case though. Also, check to see if your rubber drain plugs are still in the trunk floor (one in each well). If they fell out, there would be a good sized hole there and water could probably get in. This would be more towards the back though...