Working from the clue that you said that the underside of the body was wet after the rest of the car was dry - perhaps the rocker panel area below the door sill is filling up with water.
If the door sill will snap up, pull the carpet away from the door sill and see if there are plastic plugs in holes in the body beneath the door opening on the inside. If so. pop one out and see if the rocker panel area is wet inside. It may be filling up with water through a rust hole, or it may normally carry water from the air intake or sunroof drain, and its drain holes are plugged. If it fills up, water can leak through the plastic plugs into the carpet.