It could be the a/c evaporator hose is disconnected. Secure the drain hose to evaporator drainage tray under the dash.

I had this problem with my 98 Town Car too. When it would rain, water would flood the doors and leak out very slowly. With long heavy rains the water would spill over the metal inside the door and get on the floor. There are two drains at the bottom of the doors. Over time they became cloged with dirt. Remove the plastic tabs from the drains and the water and dirt will flow out. The tabs are easy to replace.

Did you notice the water after a rain? or was it dry?

the weatherstripping around the door may be damaged. inspect for tears, missing sections, detatched sections, use a garden hose and spray aroun the door seal to see if there are any leaks. also spray around the window to see if that's leaking.

are you sure it's water and not engine coolant? the heater core may be leaking. it is located on the passenger side under the dash. is the coolant low?

there may be a hole in the floor