In Iron Man Issue 218 we see he has created a suit, the Iron Man Armor Model 6 or Hydro Armor, specifically to go underwater in.
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In Avengers Vol 8 Issue 9 we see Iron Man Armor Model 61 which he uses specifically to fight underwater in.
In the Iron Manual we see his Deep Submergence Suit.
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In the MCU Tony's armours seem to cope reasonably well underwater. In The Avengers we see him out at sea underwater fixing the pipeline.
In Iron Man 3 we see the Hammerhead armour as part of the House Party Protocol.
It is region locked so I can't download the app but the Iron Man 3 - JARVIS: A Second Screen Experience app apparently describes this armour as:
Deep Sea Diving Suit designed for extreme pressure and traveling at high-speeds underwater. Features upgraded work-lights for high visibility.