After finishing the Way of Salvation quest, talk to Joseph in the sewers. You need to turn off the water valves, then open the floodgates. Be careful opening the floodgates, a suicider may walk up behind you.
Once you open the floodgates it will release a new enemy type, the floater. Try to use ranged attacks on him because he barfs when you get near him. If you don't have ranged attacks try to attack him from behind.
It's a long way through the sewers with a lot of enemies so be prepared. Once you reach the end, it will end the quest and start the Head Against the Wall quest.
ID Card #046 - It is directly behind the floodgate controls on a desk.
ID Card #048 - Its in a hallway to the left behind a closed door after you fight the Thug and right before the Suicider. It's at the end in a briefcase.