When fighting Ganondorf, take out the fishing rod. He will drop his guard and watch the bobber. While his guard is down, take out your sword and hit him. Repeat this until he is defeated.
Ganon will start the battle by taking over the Princess and knocking out Midna. She will fire balls of energy at you. When they hit, Midna will explain that your sword can reflect them. When it connects three times with Zelda, Midna will pull Ganondorf out of her and the next stage will begin. Ganon will turn into a large beast with a jewel in his head. Shoot the jewel with an arrow then attack his belly. He will disappear and red swirling portals will appear. One will turn blue before he charges at you from it. Continue shooting until he disappears each time you shoot him. Midna will tell you to turn into the beast. When Ganon charges again, target him and hold A, which will imitate the cattle wrestling from the start of the game. Midna will grab him and you must select a side to throw him to, then attack his belly. Ganon will appear to die but will return once more. Midna will use the fused shadows to try and kill his spirit while teleporting Zelda and Link away from harm. Hyrule Castle will explode from all the magic yet Ganon will remain. You will start the third stage of fighting Ganon with him on horseback and Zelda given Light Arrows from the Spirits. You must ride close to Ganon so she can shoot him then attack with your sword. Note: If Ganon gets behind you he will attack and knock you off then play chicken until you can get behind him again. After a certain number of hits on horseback, you will face him in a sword fight. He will teleport every so often, but you can easily roll away. The best way to kill him now is use the rolling attack from behind, then swing your sword afterwards. He will take the spinning hit and two slashes afterwards, but then block the rest. After this, Ganon will be defeated.