Jeep YJs with the 4.0L EFI I-6 came from the factory with a scoop attached to the front of the airbox (immediately behind the driver's side headlight). This scoop, designed to draw air into the engine, has a known tendency to draw in water splashed onto the grill, usually resulting in engine damage.
If you still use the factory airbox, Chrysler recommends that you remove the plastic scoop from the front of the airbox (it should come out easily) to reduce the possibility of drawing water into the engine. I actually went a step further and completely blocked off the hole in the front, drilled a new hole into the side, and attached a piece of radiator hose to that, so the air is now drawn in from just below the hood (the TJ airbox does a similar thing). I also drilled small drainage holes in the bottom of the airbox (the unfiltered air half) to prevent standing water from building up inside the box.