its like plastic piece above the wheel by the fender i was wondering if it was ok to take that off or if it would put water up into the engine bay

 

I've heard of people taking it off. First off if you have a CAI I wouldn't take the right one off because you might suck water in.
I wouldn't take them off personally because you would get more crap in your engine bay plus it would get more water and crap on the metal causing rusting.
Plus you will get crap behind the bumper.