Um help. How did the water get there?

So basically my cobalt is having more problems than it's worth. It's a 2008 LT coupe with 120,000 miles on it. I'm trying to stick it out for a two/three more months but is there anything cheap or temporary I can do to help. Here comes the laundry list: - traction control light randomly turns on. Doesn't matter how long or short it runs. It comes on randomly and says to service. - exhaust leak with o2 sensors misreading - fuel line leak it's completely rusted - and here's the part with the water. The compartment where the button to open the trunk is... was filled with water. We did get some rain yesterday but still. How?? Also the motor for the sunroof doesn't work and is not open.

For some more context I have only had this car for a bit over a year. My bf has done some fuel line repair kits on the fuel line but doesn't seem to be holding up. It is throwing a check engine code for it and we've already replaced the gas cap and sprayed the maf sensor and replaced the purge valve. Sorry for the long post.