When you fight him the best thing to do is not to hit him with the master sword at all. Here is the REAL TRICK if you acquire the Bigoron sword before the water temple there is the real action. You equip with that sword once you run across and back the room and he appears near the three when he comes at you all you do with the Bigoron sword is stab he won't even get a chance to touch you at all. Since your sword is too long he cant block it or jump on it he is slow with big swords.