Runes are an important part of the Dishonored world; with their help, you can improve old or acquire new skills that will help you in the process of passing the game.
Steps
Method 1 of 3: Part 1 of 3: Getting the first three runes

Step 1. You can get the first three runes already during the first visit to the pub "Hound Pit" (between the missions "Innocent Condemned" and "High Overseer")

Step 2. Go to sleep
The first rune will be given to you by the Outsider during his meeting with Corvo.

Step 3. As soon as you wake up after meeting the Outsider, leave the pub and take out the heart (the Outsider will give it to you)
Now you can see the location of the runes and amulets. Head to the pier, jump into the water and swim to the small island on the left. Climb onto it and pick up the second rune.
Be careful - there are predatory fish in the water. Although they can be killed with a sword, it is advisable to avoid their bites altogether

Step 4. You can purchase the third rune from Pierrot for 500 coins
Method 2 of 3: Part 2 of 3: Runes in the Sewers

Step 1. The next two runes will be available between the missions "High Overseer" and "House of Pleasure"

Step 2. Talk to Havelock
After waking up, leave the pub. You will be informed that Havelock wishes to speak with you. Talk to Havelock - he will say that strange sounds are coming from the sewers, and he will give you a key.
Exit the pub through the back door, turn left and go up the steps. On the left you will see Havelock and Lord Pendleton

Step 3. Get down into the sewer
Open the hatch next to Havelock and jump down the drain. Move northwest until you spot two mourners. you see two Weepers.
- Kill or put the mourners to sleep.
- The first rune is found in an overturned cabinet next to the woman mourning.
- The second rune is under water behind an iron grate.
Method 3 of 3: Part 3 of 3: Obtaining Runes for Quests

Step 1. Duel with Lord Shaw
Before leaving Lady Boyle's estate, complete Lord Pendleton's side mission. He will ask you to find and challenge a man named Lord Shaw to a duel. After the duel, talk to Lord Pendleton - he will give you the rune.
- Lord Shaw can be found in the courtyard of Lady Boyle's estate; he will be wearing a wolf mask. Talk to him - he will challenge you to a duel.
- After you stand at the indicated spot, Lord Shaw will begin the countdown. On the count of three, quickly turn around and shoot him.
- Even if you hesitate, Lord Shaw will not kill you on the first shot. He himself dies on the first hit.
- Also, if you prefer a non-lethal outcome, you can shoot him with a sleeping pill dart.

Step 2. Have mercy on Lady Boyle
Complete the mission Lady Boyle's Last Reception without eliminating her.
- You can do this by talking to Lord Brisby: he will offer you to kidnap and give him Lady Boyle. Lord Brisby can be found in the main hall of the Boyle Estate.
- After completing the quest, return to Corvo's room in the Hound Pit Pub. A letter of gratitude from the Boyle family will be waiting for you. A rune will be attached to the letter.

Step 3. Find Emily
After Lady Boyle's Last Reception, you can get another rune by finding Emily at the request of Calista (the woman who cares for Emily).
- Go to the pub and talk to Calista. She will ask you to find Emily.
- Although Emily is hiding in various places, the first thing to do is look in Corvo's room and on different sides of the tower where Emily lives.
- The ability "Dark Sight" will greatly facilitate the search.
- Emily will give you the rune after you find it.