Probably the passenger side door and the drain holes are clogged. It will probably fix itself or you can pull the door panel off but closely follow the instructions posted elsewhere on .info.

You run a very high risk of taking out the alternator by submerging the bottom end in muddy water - my GF's literally blew in seconds as she tried to cross a deep hole. Dealer Alts are $400+, auto parts stores can get you one for about $150.