There are seals around the tailgate that may be letting water in. Best way to figure out where it's coming from is to get in the rear, close the tailgate, and have someone shoot water under pressure @ the tailgate.
Probably not possible in Canada this time of year, unless you can get into an indoor car wash and do it.
Your profile doesn't say what year Jeep you own, but if it's still under warranty take it in and see if the dealer can fix it.
From your description, it sounds like there might only be water UNDER the tailgate? If so, I wouldn't worry too much about. If it's getting INTO the Jeep, that's a different story. Look in the well where the jack is stored...is water getting in there?
If so, again, I'd take it to the dealer.
Here's a thread about water leaks, some of which deal with the tailgate. The tailgate action starts at the bottom of the first page...actually, the best way to view this is NOT use the link. Instead, go to the search section (top right of page), click on Advanced Search, type "tailgate leak" into the upper left hand field, select "JK Jeep Wrangler Forum" in the box @ lower right, the hit search. That way, the words "tailgate" and "leak" will be highlighted in red. You can scroll through the thread and read only the parts that have to do with tailgate leaks.
Here's the link anyway:
my leaking jeep