Bottle 1 -
Go to the guy with the turban on his head in Kakariko Square. Buy the bottle for 100 rupees.
Bottle 2 -
There is a building in Kakariko Village that has an entrance to the back. If you walk in the back of a building you will find a chest. Inside the chest is bottle #2
Bottle 3 -
After you can swim with the Zora's Slippers, swim under the bridge near Link's house, and talk to the homless bum there and he will give you your third bottle (Wonder what Link had to do for it)
Bottle 4 -
Inside the Village of Outcasts at the Dwarven Smithy's house (ruined in the Dark World). There will be a chest, take it to the desert in the Light World. Talk to the man by the sign that doesnt want to be disturbed and after you promise to not tell anyone that he is a Thief he will open it for you. This will give you the fourth and final bottle.