RUNE 1/1 - You cannot miss this rune because obtaining this one is a part of the first encounter with the Outsider.
The Hound Pits Pub #2
RUNE 1/2 - The rune can be found on an islet near the docks.
RUNE 2/2 - The rune is in Piero's stock (you can also buy it during one of your visits to the pub).
Mission 2 - High Overseer Campbell
RUNE 1/7 - The rune is in the basement of Granny's apartment.
RUNE 2/7 - The rune is a reward for completing the first assignment from Granny (eliminate a group of bandits). You can find it upstairs in the apartment.
RUNE 3/7 - The rune is a reward for performing the second assignment for Granny (contamination of elixir in bandits' headquarters). You can find it upstairs in the apartment.
RUNE 4/7 - The rune is in the guard booth near the Holger Square.
RUNE 5/7 - You can find the rune inside Campbell's secret chamber, in the basement of the Overseer's building. You need to smash the glass cabinet to get it.
RUNE 6/7 - The rune is hanging on the wall in the meeting chamber of the Overseer's building.
RUNE 7/7 - The rune is in the workshop in the backyard (behind the Overseer's building).
The Hound Pits Pub #3
RUNE 1/2 - The rune is located underneath the pub, close to the place where there are weepers.
RUNE 2/2 - The rune is in the sewers under the pub, near the place, where there are weepers. You need to dive to find it.
Mission 3 - House of Pleasure
RUNE 1/5 -The rune is in the secret chamber in doctor Galvani's apartment.
RUNE 2/5 - The rune is inside the deserted tenement located to the right of the Golden Cat club.
RUNE 3/5 - The rune is hanging on the wall, on the first floor of the Golden Cat club.
RUNE 4/5 - The rune is in the attic of the Golden Cat club, in one of the rooms.
RUNE 5/5 - The rune is inside the treasures, on the second floor of the Art Dealer's apartment.
Mission 4 - The Royal Physician
RUNE 1/5 - The rune is in the back room of the tenement located near the second outpost.
RUNE 2/5 - The rune is inside the safe in Pratchett's apartment.
RUNE 3/5 - The rune is inside the building with the deranged civilian in it, neighboring with Prattchet's apartment.
RUNE 4/5 - The rune is inside the tenement, and you run into it right after you reach the location that functions as the enemy's third outpost.
RUNE 5/5 - The rune is in the greenhouse in which you find Sokolov.