If the pressure in the air is higher then in the water it will not flow up into the submarine. Most submarines do not have a moon pool except in movies. Some have regular pools though. The closest you get on a regular submarine is the trash shoot which contains an upper and lower hatch, only one can be opened at a time to prevent the water from flooding the submarine. It is theoretically possible to increase the pressure inside the submarine a bit, maybe twice the pressure, and then open both hatches at periscope depth to form a moon pool from the trash shoot. But it is more likely to send special operatives through the torpedo tubes as they are bigger.
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