small lake in my rear hatch well

After some heavy rains and splashing thru some big, big puddles, I found about an inch of water at the very bottom of my rear hatch well. Then, when I removed the plastic trim to access the donut area at the back right hand side of the hatch, there was about half a gallon of dirty stinky water down there! It was disgusting!
My question is, where is all that water coming in from??? I don't think it's the weather stripping for the hatch because I've never had this happen before, and nothing else up top is getting wet. Only the bottom.
Is there some sort of drain holes down there that water could be coming in from the bottom??? This was the first time, I've driven thru so much deep water before.
Now my carpet is ruined, and I can't replace it until I figure out what the problem is. :banghead: