Pool of water under spare tire/holes next to rear struts, What do? Options

[mmmchocolate]

So...I was vacuuming my car, as i have not driven it in a few months (being at school), only to discover i have a few pretty extensive pools of water in the hatch.

What could have caused this?

I thought at first, maybe condensation, as the car has been sitting all winter/spring.
But there is a LOT of water.

I found the a plug under the spare tire. but for the two pockets on either side of the trunk, how do i drain that water?

I'm about to use a dirt/water vacuum to remove it, but my question was, how do i stop this?

TL:DR

How do i stop water from getting into my trunk?

[richee3]

Do you have a moonroof? I'm guessing the drain lines are stopped up with something.