Sian has the Atlantis Undersea Resort.
The Wars of Reaving book had a domed underwater city on Vinton, Verne, that was a Diamond Shark holding.
Dagda in the Pentagon apparently has a ton of underwater mining operations, giving rise to the Water Elemental Mining Suits that led to the Elemental suits we know and love.
Interstellar Players 3 gave us the world of Frobisher in the Canopian Ruins region, where "untold billions of Star League dollars" were used to construct large underwater living quarters for the scientists doing genetic experiments.
The Neptune Submarine entry tells us that the FedSuns was using them for base defense after they had adopted the strategy to build fixed command posts underwater to protect the vital installations from orbital/aerospace bombardment, but no word on any specific facilities' locations other than Galtor V (and after the Combine conquered Galtor V during the 4th SW, they started using the Neptune the same way).
The Solaris VII "Aquagladius" 'Mech was built to fight in underwater arenas, and Solaris VII has one: The Pool, built in the remains of a Star League sewage treatment plant.
Lackland's local marquess had underwater habitats built at the end of the 3rd SW, but apparently they weren't very financially viable yet people were still living there (and considered it to be idyllic, despite the poor education system and lack of any real industries).
Far Reach in the Chainelane Isles had lots of underwater habitats and facilities in the Star League era, as they were a corporate hub of the RWR. However, they failed over time after the RWR collapsed.
Shimonita in the Combine had underwater mining facilities put in place by the Ozawa Mercantile Association (before the Kuritas took power), but they were rendered useless within a century due to poor maintenance routines and violent weather.
Apostica in the LyrCom had an underwater research station.
Helen in the DracCom had a large floating scientific research stationed called Aquanis in the Star League era, but it sank during the Succession Wars and is a popular underwater tourist attraction. Not sure if this counts for your purposes but I thought I should add it just in case.
Repulse in the CapCon is portrayed in the apocryphal German-language novel Gier as a frigid ocean world with domed underwater cities such as Guandoa.
Caselton in the FedSuns has several underwater and underground command centers and military bases.
Gravenhage in the DracCom was once a tropical planet with oceans before its desertification, and apparently hosted at least one underwater Star League research facility.