#1) When the mission begins, go up to street level and go to the left, where you'll find some stairs to some higher ground. To your right is a building and there's a doorway where you can get inside. Go up the stairs until you get to an open doorway, so go inside. You will find a Weeper in the same room as the Outsider Shrine and Rune.
#2) This Rune is located in the waters, on the far end from where you start. From Samuel's boat, hop in the water and swim straight ahead, all the way until you find a set of stairs. You'll find it in the water near the stairs.
#3) This Rune is located inside of the Boyle Estate, in the basement and behind a locked door. The key for this door is located upstairs, in one of the bedrooms, which you can tell by the different looking doors. You can get upstairs by going in the ballroom (the one with all of the food), where you will see a doorway with stairs leading up and down. Once you have the key, go downstairs into the kitchen and into the basement; the first door can be unlocked by using the nearby switch. When you get to the door requiring the Basement Vault Key, open it up and you'll find the Rune inside.
