I wouldn't suggest slowing/creating difficult terrain EVERYWHERE. That actually makes combat LESS exciting because no one can move at all. You might, for instance, offer islands of debris floating in the water that Pcs can jump from one to the next.
Consider weakened floors (stress from water pooling on an upper floor, mold/rot, etc) causing areas to collapse during battle. Also Falling/collapsing ceilings.
Weak areas in the piping - any damage to a wall would cause a rupture, and a flood would wash everyone down the pipe.
Flooded areas requiring full-immersion swimming to get to an area. (Add in aquatic enemies from the ocean's depths?)
Limited/thin air in spots; must move to get fresh air. The longer the fight, the thinner the air gets. Especially if fire is used (as it sucks up air).
Highly pressurized pipes (any damage causes a rupture, sending shrapnel and contents everywhere).
Missing stairs/etc where the party must "make their own path" by destroying the room.
Precarious rope bridges suspended over several hazards (or connecting islands of safe terrain). Perhaps the rope bridges don't even have the rope handles (terrain requires an acrobatics check to traverse safely without falling). Any damage to the bridge will cause it to break.