2006 Lincoln Town Car has water accumulation on passenger side rear floor

Check all your door and trunk weatherstrip seals, sun/moon roof (if you have one), check all the channels that funnel water off roof aren't blocked with debris, like leaves and such. I don't think you have a rear heater core, but if you do, you should be able to tell the difference between coolant and water. If you absolutely can't find source of water, go to the parts store and get the little dye packs, these are little differently-colored tabs you put on the outside of the car, then spray the car with a hose, if that area leaks you'll know it on the inside (don't worry it cleans up easily.) Put one of the tab over the rear door, spray it, if the dye shows up on the inside, you found your leak. Use the different colors so you don't confuse just where the water may be leaking from.

Open the hood on the right side where the blower motor vents there is a little rubber flap. It is clogged causing water to drain into the vent. The water runs down on the inside of the fire wall under the carpet ending up at the lowest point which is the right rear floor. It happens when the car is parked in heavy rain. Also if the seal in damaged it will cause it to leak. Remove the plastic and remove you will see white around the seal if it has been leaking. Easy fix go to home depot buy Frost King Rubber foam Weather seal 3/8 wide 5/16 think 10' long peel old off clean apply new and make sure seam in toward the engine. At seam apply black weather strip adhesive let tack for 15 minutes and install.