You can make things water resistant but not completely water proof. You will most likely need a snorkel on the intake to start with. Then You want to extend the vent tubes for the differentials, transmission and transfer case.
Then start with the electrical system, you will want to apply dielectric grease to all the connectors to seal them up.
Another addition is an electric fan and then an off switch so you can prevent the fan from running temporarily while going through the water.
Even with all that you will still want to change fluids as soon as you can since water will make it past the axle seals.