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 (relevant part starts at 01:29):
It is near the first Sokolov painting in the mission:
There is a painting in one of the apartments lining the flooded main street (it might as well be a canal at this point). Stand on the pedestrian bridge and place the "Daud's Base" marker ahead of you. The apartment is ahead and to your left (the one with the balcony overlooking the water). The room with the painting does not have the assassin and the Station Key, but is the one with a Weeper.
The safe combination is: