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?

[mmmchocolate]

man i hate tracing down water leaks such a pain......especialy in my car where stuff could have been helped if it was fixed at the first sign of trouble...but then again it would probly have just been rigged like some of the stuff in this car when i bought it....(i HATE going over someones work that could have been done right with alittle more effort!) i have a tiny leak i need to trace but its 1 of 3 things that it could be, broken stud from tail light so theres a hole in metal panel,goopy rubber stuff under hatch window failed, or hatch weather striping....still need to find out where its comming from...maybe ill use some water with food coloring in it to make it easier to find!...

thats where im starting....

all 3 of those options.

not looking forward to it