The D4 is very capable of driving through water, with a raised air intake can wade up to the bonnet.
If the water is dirty, like Scrubby Creek going into Elliot Falls then a tarp/bra is the best way to go. This keeps the muddy water splashing around the engine bay.
The main thing with water crossing is, obviously know the water depth.
Fast flowing, up to the hubs is generally ok to drive, but if you can't walk it don't drive it.
Slow moving or still, then the top of the wheel arch is ok.
If you know your capability then a little deeper is fine.
Most cases of water going up the windscreen is due to hitting the water too fast, nose dips in and water goes everywhere and the vehicle nearly stops, it's like doing a bellyflop, lots of pain and no progress 
 
Stop and switch off to let the vehicle cool down, wheel bearings diffs, transfer and gearbox. Let the engine cool down and the fan will not grab forward. 
I was about to make a post & read Tony V's advice, and I couldn't agree more.
I would only add as a safety factor, a walk thro' is essential, wait until another vehicle is closeby just incase. Reduce the risks increases the safety, especially if travelling alone.
Then get all 4 wheels wet, before powering through, a safe speed is a fast walking pace and create a small bow wave, see the speed in the video.
The attached video is my D4 on off-road height followed by a Toyota 79 Ute so you can get some perspective.
Low range and I tend to use Mud Ruts but leave it in drive.
Defenders excepted, water gets in only if you stop, water goes through the holes in the bottom of the doors and up through the door trim.
Bookmarks