There are total 4 bottles that you can find in The Legend of Zelda: Ocarina of Time. One is part of the main quest while the remaining three are side quests which you can trigger and get bottles as reward after completing these side quests. You can follow the detailed guide below on how you can complete these side quests and get the bottles.
In Kakariko Village, talk to the Anju on the south side of the village, who is standing near a pen and holding her head. She will ask you to find her 7 Cuccos ‘Chickens’ and reward that would be something good. (Bottle)
You need to collect 7 chickens and put them in the lady’s pen to get your first bottle. You can find all of the seven chickens in the following locations:
In front of you when you enter Kakariko Village.
Inside the box in front of the stairs.
At top of second stairs near the entrance to the Death Mountain Trail.
From the second stairs where you found the third chicken, run off the red roof next to big tower. Climb up the stairs in front of the well and turn up to the next set of steps. Jump off the ledge to the other side to get the chicken just next to the house.
In front of the stairs near the chicken pen.
From where you found the 5th chicken, walk up the nearby steps. Get close to the fence and jump to the other side. You can throw your chicken over the fence to pick it up later. It would help you jump over the fence, do it diagonally. Jump down below and get the chicken in front of the ladder. Take the stairs and throw him to the other side to pick him up later.
At the top of the ladder you come across while finding sixth chicken. Which was in front of the ladder.
As you enter Lon-Lon Ranch in the past, take the door to your left. Inside you will find Talon sleeping in a room full of Cuccos. Wake him up and he will ask you to play a game.
To get the bottle #2, you will need to play Talon’s Cucco game at Lon-Lon Ranch. You will need to locate three special chickens in the pile and he will reward you a bottle with Lon-Lon milk in it.
It’s part of the main quest so you can’t miss it. Princess Ruto has left a bottle under water with a letter. Drive down and retrieve it with a letter. Show that letter to King Zora, he will let you keep the bottle.
Once you have saved Epona and have acquired Fairy Bow, you will be able to take this side quest which requires you to collect Big Poes. Ride Epona around Hyrule Field and shoot these with your bow. Talk to their souls and collect them in bottle.
You need to collect Poes from Hyrule Field as Adult Link. Take your captured poes to the ghost in Hyrule Castle Town. You can find him inside the first door on the right when you first walk in Hyrule field.
You can find all Big Poes in the areas specified below:
Big Poe #1 Location. Go towards the Southern side just when you exit the Hyrule Castle’s gate and follow the sign.
Big Poe #2 Location. You’ll find a stream at the Western Side of the Hyrule Castle, just follow the stream and you’ll find it a little away from it.
Big Poe #3 Location. Go to the Lon Lon Ranch and find an alone tree on the northern side. Ride on that tree.
Big Poe #4 Location. Go to the Southeastern side of the Gerudo Valley and find a fork, the Poe is just there.
Big Poe #5 Location. Go the Southeastern side of the Gerudo Valley again and where the fork is on the path, head towards the Northern side and look for a lone tree.
Big Poe #6 Location. You’ll find a rock at the Y shaped path in between the Lon-Lon Ranch and Kokiri Forest. The Poe is on it.
Big Poe #7 Location. Go towards the Southern side of the rock which you found at #6, find a small area of grass which is next to the tree. It is on that grass.
Big Poe #8 Location. Go towards the western side of #7 and look beside the yellow trees.
Big Poe #9 Location. Look between the tree which is in front of the stairs and the mountain cliff. (Kakariko Village)
Big Poe #10 Location. Lon-Lon Ranch, go towards the Eastern Side and look for a stone wall which looks like a boomerang. Find the Poe near to that wall.