Alternator is a problem. Not sure about latest models, earlier Toyota alternators would shut down when it detected a short, thenwould work fine once dried out. Many if not most alternators on other cars will simply fry the regulator if you dunk it and you need to carry a spare.
But uh, fording a river to hood height is NOT a "small river" and worse than anything in the engine bay is you will flood the interior and likely short out the computer! You shouldn't ford anything that is above the bottom of the doors unless you are driving a real don;t care junker and or have done a TON of actual water proofing.
I have forded rivers near the door line, but not near the top of the wheel wheel, way too likely to get inside. ()And of course no snorkle on mine
)
(I do agree that the alternator at the bottom is lame, thinking about moving it on my truggy)