You had to transform a particular enemy into a piece of materia which allowed you to breathe underwater. Emerald Weapon was a tougher nut to crack than the feared Ruby Weapon IMO.
There was still a 30 minute timer though when fighting the Ultimate Weapon though, and as close as I came to killing him a few times, I just could not do it.
I remember reading a strategy around about the time the game came out (1998!?) that showed a full proof method on how to set up and then sit back and watch it do everything automatically, but it required each player to have certain materia and HP points etc.
I waited till I bred a Golden Chocobo, which took months, then made my way to the secluded cave out into the ocean and fought the boss and obtained the Knights of the Round Summoning, but even with that, Reflect, Haste etc cast, I still could not beat him.
I really do regret not trying harder, but I put a solid 3 months into that game, playing it every day, and I eventually gave up on him.