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Endless Ocean: Blue World (for the original Wii):

https://kotaku.com/5477173/endless-ocean-blue-world-review-the-wii-game-youre-wrong-about.

Incredibly relaxing and it was surprising that you could get a game that big (in terms of number of different environments) to look that good on that console.

X-com: Terror From the Deep.

Banjo-Kazooie. Nothing put the fear of god into 8 year old me quite like that goddamn shark.

Underwater scenes are common in LucasArts Games. I can think at least of Monkey Island 1 & 2 and Indiana Jones and the Fate of Atlantis.

The one in Monkey Island 1 is absolutely hilarous and is full of Easter eggs.

Ecco series for best music.

Grim fandango!
Terror From the Deep too,
... can't think of anything else.

I agree with those who mentioned Terror from the Deep, also that underwater part in Monkey Island 1 is great. :)

I always liked the part in Another World where you go underwater... also another part where you have to run from a bunch of water after bursting a hole on the pool wall, which is one of my favorite moments of that game.

Another favorite is The Cave (sadly not available here on GOG), I love the underwater parts... and if you bring a certain character, you can even swim in a pool that looks the same as the one in Maniac Mansion. :D

Swimming in the fishbowl level in Alley Cat (another game I wish we had here) was also fun.

Always considered Subwar 2050 a perfect exemple of this. It had an underwater feel that was absent from, say, the Aquanox series. Which felt more like vaguely darkened flying saucers flight simulators by contrast.

The submarine sim Cold Waters does it perfectly.

TR Underworld

Kind of a limited clip. Anyone who has played the game knows how much more extensive it gets.

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ABZU, Silent Hunter series, a bit in Giants: Citizen Kabuto.

Sub Culture and Archimedean Dynasty.

And the upcoming Aquanox: Deep Descent looks promising.

I also want to ask everyone to upvote everything Fairfox posts please, this unnecessary downvote trolling is starting to make me sick.