Waterblight Ganon is encountered at the end of the Divine Beast Vah Ruta dungeon, and he definitely brings a challenge to the table. I am going to outline the method that worked best for me, but it will probably take a few shots to take down Waterblight Ganon. First step is preparation. Seriously make sure you have a few decent bows and a couple spear or staff like weapons. Bring plenty of food and swing by a couple shops to buy all their arrows (fire and bomb arrows do the most damage here). That’s right buy all the arrows you can you don’t want to run out when Waterblight Ganon has less than a quarter of his health left.
Now that we are ready let the battle begin. You want to equip a spear or staff so that you have some reach when it’s time to attack in this first phase. Stay within striking distance to keep Waterblight Ganon from throwing his spear at you. Use cryonis (the entire floor is currently water) and stand behind the pillar of ice, as Waterblight Ganon attacks his spear will break causing him to move across the room follow him and get a few strikes in as he repairs his spear. Repeat this process until Waterblight Ganon has lost half of his health and the battle switches to phase 2.
The water is now deep enough to swim in and there are four platforms in the room. You want to stand on the platform opposite Waterblight Ganon, and once again stand behind an ice pillar. Ready your bow as Waterblight Ganon hurls a block of Ice into your ice pillar and take a shot. Repeat this process until the number of ice blocks being thrown increases. At this point you can actually drop off the back of your platform into the water and all of the ice blocks will smash into the platform before ever reaching you. Jump up to the platform in between sets and shoot an arrow at Waterblight Ganon until his health is depleted. If Waterblight Ganon falls from the ceiling at any time after the first phase of the battle be sure to run over to him and attack while you can.