One of the qualities that makes the Jeep Wrangler such a better offroad vehicle than just about any other 4x4 and SUV on the market is its water fording capability. Jeep publishes a water depth rating of 30 inches for an unmodified Wrangler thanks to its high-mounted engine air intake and axle, transmission, and transfer case breathers. Most other vehicles are much more vulnerable in much shallower water.
Jeep makes a big deal out of the Wrangler's water fording ability, and they produced this video to illustrate its capabilities:
The latter part of the video shows and discusses proper water crossing technique; it's unfortunate that the video's introduction glamorizes excessive speed, which can not only damage the vehicle by allowing the engine to inhale splashed water, but which also causes excessive erosion to the riverbed.
Proper deep-water crossing technique is demonstrated in this video:
Keep your speed down to minimize splashing. If water enters your engine's air intake, it can be sucked into the cylinders. Water doesn't compress like air does, so if you're lucky you'll simply stall the engine. More likely, you will bend a connecting rod or punch holes in your engine block. Matching the speed of the bow wave also helps keep water from entering the drivetrain where it contaminates your gear oil. If not immediately flushed, water in your gear oil can cause rust that damages critical bearing and gear surfaces.
Proper water crossing technique will allow your drivetrain to stay safe in water deep enough to trash your Jeep's interior. Drain plugs in the floor help with the draining and cleanup, but the carpets will be ruined. Most 4wheelers who regularly cross deep water or mud holes will remove their carpet and replace it with Dupli-Color's brush-on, roll-on bedliner product that makes a terrific waterproof alternative to carpet. Its textured finish also looks great when applied to bumpers and fenders.