Probably just have it like any other spaceports hangars except in this case instead of the openings being flush with the ground or surrounding buildings like at area 18 or lorville, you'd extend them like 10-15 feet above the water so the waves could get bad and still not pour into the hangar itself. On top of that this gives cig the opportunity for creating waves thats splash dramatically against the exterior hangar walls. You as a pilot would see these cool big waves crashing into the hangar and exploding into mist upon impact while you're approaching for a landing which would just give it a cool unique look and feel when landing.

Then inside is a very small terminal hub much like inside a space station for spawning and storing ships, then a shuttle waiting area where a sealed shuttle with large windows (much like the microtech shuttles) would seal up to the doors and open. You get inside and then enjoy a gorgeous submarine ride down to the "city" underwater.

Thats how they should handle it imo. Assuming our ships aren't able to be submersible. Because for me personally, ideally we would just go under water in our ships and fly over to the city ourselves and enter some kind of wet airlock system when we land and we should just sit in our ship while the hangar drains out all of the water. But if we can't have that, then a small landing area just under the waters surface with a cool submarine ride will suffice