2007 Lincoln Town Car, water sitting right rear inside door mat after a heavy rain ?

You have a door or engine compartment seal which is toast.

Barnes is correct. I have worked as a mechanic for 35 years and the best way to find a leak is to have an assistant spray water at the suspected area while someone is inside to actually see where the water is coming in. Water can come in one area but puddle in a different area so the best way is to have someone blast water at the vehicle and watch from inside. Door seals and even body seams are the most likely points of entry but I have also seen the belt molding (the thin strip of rubber that rests against the glass) allow water to get inside the door and then trickle onto the floor.

Hi suggest you have the windshield surround replaced as the rubber silicon has persisted.

Bad or missing door seal.

Close the window.

Door seals are suspect. Sit in the car and observe whilst someone plays a garden hose around the closed door. Another method is to shut a piece of paper in the door at various points. If it pulls out with no resistance a new door seal is needed.