This is really common. If you look at the passenger side firewall up behind the valve cover, you will see a plastic snout thingy sticking off. It is the drain for the air inlets. Sand, leaves and all other manner of crap clog it up, and prevent water from draining (well, it still does just not where you want it).
I just stuck a small screwdriver up it and cleared the shit out. You CAN pull it off, but getting it back on was a pain in the ass, and sometimes the rubber rips when it becomes old & stiff. Good muck man.