2000 Ford Taurus SE, water in spare tire res in trunk. Any suggestions on

Either the trunk seal is leaking or there is a small rust hole in the lip that the trunk seal is attached to. (Look under the pine straw and leaves)

That is the only two ways water can get in there unless you have exploded some Deer Park Spring water bottles.
 
Put an assistant in the trunk with a flashlight, close the lid and put the garden hose to it.
They'll let you know where the water is leaking in - and in just a few moments.
 
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