believe it or not the rigs are designed to take this kind of abuse.... the only thing you're going to want to keep an eye on is suspension over heating.
Toyota officially notes as well that the trucks are safe to ride in up to 27.5 inches of water before claims will be denied on warranty issues. I dont know about you guys, but if you go measure 27.5 inches on your rig your going to be surprised just how deep the truck can go before water comes in or does damage.
I tried finding the video on YouTube (no luck finding it sorry) that I had watched years ago but Toyota actually did a promotional testing video on the 5th gen 4Runner a while back where they actually give instructions on proper driving through water that was as high as the top of the wheel well. I remember them saying to keep the car always in a moving motion so a wake of water would be pulled down from teh engine bay, giving less risk of water logging the engine etc...
its pretty interesting to be honest that such a piece of equipment is designed to handle so much abuse.