This fight is divided into two stages:
Your priority is shooting the blue crystal on top of the enemy's head. This boss is rather slow and you can attack him with your sword as well. Mind its attacks with the long spear, though. Additionally, when you're right underneath it, the boss will charge the spear and slam it into the ground, dealing damage all around the area. When you see the weapon being rose, get away to avoid damage.
From time to time, the boss will turn into a blue sphere of energy and will proceed to another area of the location. Follow it and attack the whole time; when the boss loses 50% of HP, stage two will begin.
The boss will rise the level of water in the room, which will make the fight more cumbersome. Fortunately, there are still four platforms from which the enemy can be attacked. Use your bow again and try to hit the blue crystal on its head. When Waterbligh Ganon closes in on you, swim to another platform and continue shooting at the boss.
The boss will summon more ice projectiles and fling its weapon at you, so be careful. When you hit it a couple of times in the crystal, the enemy will be stunned - quickly get to the platform it's at and attack. The boss will soon get back to senses, but with much less HP - if you've done everything correctly. Repeat this procedure until you claim victory.