Bottle 1: Sera gives this bottle to you with milk at the beginning of the game.
Bottle 2: Purchased from Coro South of Faron Forest for 100 Rupees (includes Lantern Oil with purchase).
Bottle 3: Go to the Fishing Hole that Hena owns at the place called Upper Zora River. Go to the Fishing Hole and bobber fish at the bridge where there is a sign. The water is murkier than normal. This may require multiple attempts.
Bottle 4: Defeat and collect 20 Poe Souls and bring them to Jovani in Castle Town (all the cats must be able to dig where they are).