Underwater Combat

One thing to keep in mind is soundwaves and shockwaves travel through water for a long distance. So audio cues where someone/something is will be very off. Similarly, explosives have likely much larger blast radii

Oxygen supply or a way to breathe underwater will be needed, so the characters can live

Water drag will be another problem, anything that causes drag will cause problems. Physical shields (like a Medieval knight would carry) would have to move through water edge on, as moving the flat face through water will be difficult.

Water conducts. So if you have electrical equipment, a small crack that you would ignore on land can cause your battery pack to short out. If that is providing power for your underwater vision gear, you are now blind. If that is providing the power for your underwater power armor, you might just electrocute yourself.

Waterlogged stuff. Trying to find books in a submerged city? You have goop instead. Better hope that the ink in the books was not water-soluble, otherwise you just have blank pages.

Rotted stuff. Wooden shingles, supports, and other wooden material that is fastened in place would become waterlogged and soon start rotting. This means a wooden roof will not keep the giant shark away from your bleeding characters.

The 3D movement would definitely be a change. Instead of the characters ascending through a submerged castle defeating the traps/hazards one floor at a time, the characters might just go into the top window and work their way down. Going from the top of one tower to the top of another tower is a relatively quick swim, as long as both have openings.

Currents. There can be currents flowing, with the characters being flowed gently downstream and unaware of the effect unless they are paying close attention to their surroundings. Indoors the current might go through a choke point and pick up speed, so some passageways might be impassable from one direction during part of the day (and on the other side of that passageway, anything in the way will steadily get sucked through).

Barnacles (with their sharp shells) can be a serious threat here, as the characters get scraped by a wall covered in barnacles, causing wounds, and getting the local sea life agitated from the blood in the water. Leading to a famous quote, "Thank goodness all the fish cleared out of the way, now I can see the other side of the room. Wait, why are the fish hiding?"

This is an exploration into a maze that has a hostile environment both between the characters and at the destination. It will take time to explore the entire area, putting together clues, backtracking due to a wall having fallen down, avoiding the hungry shark(s), and all of their gear has to be on a boat. If they forgot a piece of equipment they need to either make a replacement, use something else, or go without.