Jeep Grand Cherokee wet passenger carpet and water in battery compartment.

I have a 2011 Jeep Grand Cherokee and have had
the vehicle since 2012. Issue started roughly 6
month ago when I heard an audible sloshing noise
when I would break or turn coming from the
passenger side area. Upon inspection I found
standing water underneath the passenger seat in
the battery compartment. I researched online and
removed the two black plugs from underneath the
vehicle and drained a large amount of clear water. I
had had issues with my last windshield being
sealed properly and since mine had a crack I went
ahead and replaced the windshield thinking it was
a seal issue there. I left work late last night from
the hospital, we had had a hard rain all day and
again I heard the sloshing noise. My father and I
tried to trace where it was coming from but only
found saturation of the carpet under the passenger
seat that looked to be trailing to the front of the
vehicle. I don't have a sun roof, it's been cold these
past few months so I run the heat with my two
kids, I have absolutely no idea what to do and
would appreciate any help and direction if
possible.
Thank you I'm advance