In Central Rudshore of the Flooded District before entering the Daud's base there is a safe in the flooded basement of a nearby building. Where am I supposed to find the combination of it in-game?
The combination is found in a letter, upstairs in the Rudshore Waterfront Upper Level. See this video on how to get there:
It is near the first Sokolov painting in the mission:
The safe combination is: