Same protocol driving an M/T.

I actually find AT better than MT when fording floods, one can focus more on the roads and not worrying with the gear. Also, MT has the tendency slipping the clutch when flooded.

Similar damage in case water breached powertrain & transmission. Hub-height flood fording is safe, but going beyond could flood breather tubes of tranny/transfer. Having a milky-colored ATF is a sign of water breach in your tranny..