you may want to look into some things you can do to protect your vehicle from damage before going swimming. Its a well develop topic on here.
They might give you some insights on whats wrong. i would stop driving a hydraulic based transmission when full of water. as it boils and vapours which i great for your valve body. dirty water is even better because when the water evaporates and vents out you will have two problems, one a huge amount of dirt in your valve body and not enought trans fluid to operate correctly, maybe drive not lubricate the trans.
Im sure that anything with a vent and lube will have dirty water in it, both diffs, transfer case, transmission, etc