After you have crossed the tracks, drop down to the road and take the alley. Look for the first underwater and second on top of the cabinet. You will find the first in the sewer under the Hounds Pit, near the two Weepers just past the gate. You will find this rune inside a picture frame hanging on the wall. After entering Overseer’s Mansion, look over the fireplace where Campbell and Curnow have their meeting. Get inside and you should find the rune on the table. When you are disabling the Walls of Light in the Distillery District, you will find this rune in the guard station on the left side of the road beyond second Wall of Light. Go forward and you should notice shining lamps. You can reach it by exiting through the gray door on the first floor of Granny Rag’s apartment, into the alley. You will find this rune behind Granny Rag’s apartment, in the crotch of a shrine.

Once you have done that, Granny will reward you another rune and you can retrieve from the same place on the second floor. For this favor, you will have to get a rat viscera from Dr. Come back to Granny after retrieving the first rune and she will ask another favor.

You will find this rune hanging over the fire on the second floor of her apartment. When you meet Granny Rags in her apartment in Distillery District and help her get rid of the thugs outside her house, and she will reward you with this rune.

Dishonored 2 mission 7 3rd rune