Is it only when you are driving it? or even if the car sits in the rain? If its only when you are riding in it, one or more of the floor plugs might be out and kicking up water into the hole.
If it happens when it also sits, check the vents. There is a drainage tube that might be clogged, if it clogged water is sent into the heating/vent system. Its a black hose that comes out of the firewall near the battery, should be able to pull it off and clean it out.