When I open the hatch after it rains, water drains from here. Now that I see the picture it looks like a little bit of rust forming:




Once the door is all the way up it runs out of the trim on the sides of the back window:



My only guess is that it is leaking through the windshield wiper hole, or the rear window is leaking. The cargo area is bone dry. Until I raise the door

 

I can actually hear the water running through the door as I open it

 

Does your boot seal when you close it? I had a bent hinge, and others have failing, broken hinges, and the boot doesn't seal right. Otherwise, there's obviously an opening somewhere that is causing it. What year is your MINI?
If it's still under warranty, shouldn't be too hard a fix.
If not, maybe something you can DIY! More time to spend with your MINI! IMHO never a bad thing!

 

I have a 2004 R53. Similar problem. It was the seal on the hatch handle.
Easy fix. Take off the handle, if it's in good condition then just clean up the area and put back making sure to tighten the fasteners properly.
Or replace the gasket if it needs it. A little sealer doesn't hurt either.

 

Am I the only one that doesn't have that drainage hole?? I have an 05 non S

 

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Gasket for grab handle is part no. 51-24-7-114-521 - About $13.00 from MINI.

If no dealer nearby, then cleaning it up and adding some sealer will be good for a while.

 

Are you talking about the little pad that you press to open the rear hatch or the trim above the license plate? I'm wondering because this problem just became apparent to me. We've been having a couple worth of days of rain here in Texas and I have noticed my rear hatch is holding water. It collects if it sitting or driving and I can hear it slosh around in the rear hatch when I turn. When I open the rear hatch it proceeds to rush down the plastic trim and pour all over the inside of the boot and plastic trim, around where the boot light is. Pulling the trim tomorrow and checking seals, especially the high third brake light as that seems to be a common culprit.

EDIT: Just checked and I do not have that drain hole. What year is that?

 

Thanks guys,a little sealant did the trick!