If you hover above the water not moving, with just your wheels in the water and nothing else. The helicopter Engine will start to take damage and then get destroyed.

Helicopters in real life have both the air intakes AND exhaust on top of the helicopter so they can go quite deep in the water and as long as the rotors are not hitting the water the engine will continue to run just fine.

but obviously they can't go so deep that the cockpit begins to fill with water