Overall, arrows are the best way to do damage to Waterblight Ganon, especially if you aim for his blue eye. If you have any Shock Arrows left, this is the time to use them. Bomb Arrows, or even any other elemental arrows you have will also a decent amount of damage
Zelda: Breath of the Wild's Waterblight Ganon is the boss of the Vah Ruta dungeon. Waterblight Ganon telegraphs his attacks — mostly a thrust, a spear throw and if you get close enough. it’s weakpoint is it’s eye