2006 Chevrolet Equinox Wet floorboards

I have water accumulating on my floorboards as well as the spare tire well. I understand that the most common cause for this is clogged drains from the sunroof and such, but I am curious as to if an emissions control issue or problem can be causing this as well. We have recently replaced the EGR valve, but still have a check engine light. If this is emissions relating what would be the cause and solution to such problem?