When he's close, he may thrust his spear. Side hop this and there's a chance of a flurry rush, which takes down a lot of health. When he's close and you see him raise his spear up, just run so the shockwave doesn't hit you. When he's not too close or far, he'll most likely sweep his spear, which will be signified by him pulling his arm out to his side with his spear in hand. It's best to backflip to dodge this, and once again perfect timing will get you a flurry attack.
At long range, he'll throw his spear at you. To dodge, just move to the side, if you stay close he won't use the move at all. Once you do a bit of damage, he'll fall to the ground. I would recommend using the best sword you have to do damage. After you get him down to half health, Phase 2 starts, which is much harder. The water level will rise, and the 4 platforms are all you have to stand on. Waterblight Ganon will also focus on ranged attacks. At this part, he'll throw ice blocks at you, so you can use Cryonis to break them or just dodge them. At this point, it's best to not use melee weapons and just stick to the bow and arrow. Using Shock, Bomb, or Ancient arrows will do the most damage. When he swaps to the Guardian-like beams, it's best to dodge them, but you can perfect block and parry them to send them right back at him. When you defeat him, you get Mipha's Blessing, which acts like a second life. It fills up your heart container and gives extra hearts.