Empty Bottles Guide and Locations
As we have known for almost two decades one of the rarest and most valued items in all of Hyrule is... a bottle. Twilight Princess is no different as there are a total of four different bottles for you to collect in the game. One of them is acquired very early on in Ordon Village and is given to you from progressing through the game normally.
The other three bottles are all side quests that you must complete on your own outside of the normal story of the game. Arguably the second bottle isn't really a side quest and you get through normal game progression too. Regardless this guide covers all four!
First Bottle Location (Ordon Village)
The first bottle is acquired in Ordon Village extremely early on in the game. After you get the Fishing Rod you will want to fish nearby the docks where the potion store owner's cat can be found. Catch two fish and the second one you catch will begin a brief cinematic where the cat returns the fish to the owner's house.
After you see that scene run back to the Potion Shop and speak to Sera. She'll be delighted the cat returned and give you a bottle filled with milk. After you finish the milk the bottle will be yours to keep!
Second Bottle Location (Faron Woods)
In northern Faron Woods you'll find a man named Coro who will sell you a bottle of oil for your latern for 100 Rupees. You can get this bottle extremely early on right after you clear the Twilight from Faron Woods and return to your human form.
It's extremely common that you get this bottle through normal game progression so I won't go into much more detail about it. Just use my pictures to find Coro and speak to him if you somehow missed it.
Third Bottle Location (Upper Zora's River)
For this bottle you have to go to the Fishing Hole which is found in the northern portion of Upper Zora's River. You can see the door to the fishing hole in my first screen shot above. This place not only has an Empty Bottle for you to find but also there's a Piece of Heart you can find as well as a Fishing minigame.
Let's stick to the bottle for right now though. Once inside you'll want to follow the mass of land around towards the northern end. Eventually you'll come across a sign that says...
Do NOT Toss empty bottles or cans here!
Keep the fishing hole clean!
This is the same sign that's shown in my screen shot below. You'll want to fish in the little pool just behind this sign - the same one I am facing in my screen shot. Apparently someone ignored the sign because doing so will reward you with an Empty Bottle!
Fourth Empty Bottle Location (Castle Town)
For this bottle you have to participate some in the Poe collecting side quest. About midway through the game after completing Lakebed Temple and shortly before getting the Master Sword you'll stumble across a man in Castle Town named Jovani and inside of his house will be a Poe.
When you kill it he'll thank you for doing so and tell you to free 19 more for him and he'll give you a reward. There are a total of 60 Poes in all for you to collect but collecting just 1/3 of them will get you the Fourth Empty Bottle.
I recommend you hunt Poes in the Lanayru Province as well as the Eldin Province. You'll get pretty much all the poes you need from these two places and they're pretty easy to find Poes too. If you've already cleared Arbiter's Grounds and have access to the Gerudo Desert you'll find a bunch of easy Poes there too.
The bottle comes with Great Fairy's Tears in it which is a consumable that restores your health and boosts your attack power - pretty nice prize for 20 measly Poes!