Mission 7: The Flooded District
When you are in the refinery getting your gear, you will lower a drawbridge and climb down a chain. Once you climb down the first chain, you can use a valve wheel to open a large door to get outside. Directly across from you on the ground outside will be the first rune.
When you get Daud’s key after confronting him, return to the door next to the entrance to the assassin hideout and go through the door you can now open. Climb down the chain and at the bottom will be the rune.
Go to the last building to the left side just before the train tracks and hop out the window to the adjacent building on the left side. Continue upwards to the roof to find the rune there in the open.
Rune 7-4 / Outsider Shrine 7-1
When you run into Granny Rags in the sewers, help her cook Slackjaw and she will leave you this rune on an Outsider Shrine in her room atop the stairs in her small shack.
After you get the sewer master key from either Slackjaw or Granny Rags, return to the entrance of the sewer and open the gate. You can then go forward and on the lower level find the rune there.