This one's pretty easy to find. Simply buy this from the man in Kakariko Square for 100 Rupees.
Bottle #2
There's a pub in Kakariko Village. Outside, you'll notice a break at the top of the hedge surrounding the building. Walk through that to enter a secret back door to the pub. Open the chest inside to get this bottle
Bottle #3
Once you have the Flippers, swim underneath the bridge to the east of Link's House, then climb ashore and talk to the camper to receive your third bottle.
Bottle #4
Go to the ruined Blacksmith house in the Village of Outcasts in the Dark World, and check out the chest. It's locked, but now it will follow you around. Take it to just outside the Desert in the Light World, and talk to the man by the sign. Ignore the sign's warning about not disturbing him and start chatting. After you promise not to tell anyone else that he's an ex-theif, he unlocks the chest, which contains this bottle.
