The carpet gets almost an inch of water in the back and the carpet gets damp in the front of my 1996 Pontiac Bonneville everytime it rains but the seats do not get wet at all any ideas?

The fact that the seats do not get wet contribute little except to suggest that the leak[s] is not in the roof, and is probably LOW. There obviously is a leak, which could be anywhere including [but not limited to] these locations. 1. The most probable is "plugged up" DRAIN SLOTS in one or more of the DOORS. Rainwater which gets into doors via the bottom edge of the window openings, is NORMALLY allowed to drain through two to four SLOTS in the bottom edge of the door. 2. The lower edge of the seals around the front and back Windows. 3. Any of the SEALS AROUND the doors. Based on your statement that the water pools near an inch in the rear, and only dampens the front carpet, suggests that the leak is toward the rear IF the condition occurs WHILE the vehicle is LEVEL. If the vehicle is parked such that it slopes toward the rear, the the leak could be anywhere. I suggest first that you check and CLEAR all the door drain slots. This is best accomplished using an OLD thin bladed knife [like a table or steak knife]. Open the door, lay on the ground next to the open door, and carefully examine the bottom edge of the door. You should be able to spot the drains, as they appear as narrow slots right along the lowest edge of the flange of the outer "skin" of the door. Insert the knife upward into the slot and "saw" it up and down in the slot WHILE ALSO moving back and forth from one end to the other of the slot. This will break the blockage up, allowing trapped water to drain [be prepared to move out of the way fast]. This will allow SOME OF the dirt to drain out with the water. If the door is dry, with a garden hose, run water along the lower edge of the intersection between the window, and the bottom of the window opening in the door. If the door is open, and the drains are clear, the water will drain out of the slots, carrying some dirt with it. If there are large pieces of debris, like twigs, small gravel, large rust flakes, etc, these will not be able to pass through the slots, but their displacement and the flushing out of the dirt will probably allow the drains to function properly. IF you want to remove the large debris, you will have to remove the door inner panel[s] and remove the rest by hand. Good luck.j3h.