This spoiler free page of the guide to The Last of Us 2 has information about the locations for all safes in Seattle, Day 3 chapter - when you are playing as Ellie. In addition to the locations of the safes, we present solutions to puzzles in which you find the right safe combination and inform about the contents of the safes.
List of safes in the Seattle, Day 3 chapter
In Seattle, Day 3, when playing as Ellie, you will be able to find only 1 safe:
1st safe - the Sunken City stage
Safe in the Sunken City stage
You can find the safe soon after you steal the boat. Ellie reaches the closed grate shown in the image. The safe must be reached before you lift the grate and move on.
Step out of the boat, take the stairs on the left and reach the upper balconies. You will find a corpse in the room - there will be a note with a combination for the safe.
Now look for the cart with wheels shown in the picture. Move it to the right to unlock a narrow passage. Crawl through it.
Jump over the window. You have to jump into the small enclosed area shown in the picture.
The safe is here - its code is 70-12-64.
Inside it, you will find supplements, scrap metal and ammunition.