Starting the map, drop down into the sewage, follow through the only open tunnel, turn left at the "Y"-shaped intersection and go through the door. Enter the room with piled crates and hit the switch. Return to the previous room (with the door) and you will notice that a staircase has been built up. Run up to the top, turn left and straferun to grab a seemingly unreachable soulsphere sitting atop a pillar behind the monitor screen. Due to its complicated location, the secret may need a few tries to acheive.
After activating the staircase mentioned above, hit another switch to open the other door from the "Y" intersection, follow the path to the lift and ride it up. Turn right, then turn 90 degrees left twice. You will see, to the right of a shotgun shell box, a part of the wall that has some pink/red broken wiring. This wall, which is actually another lift, takes you to a small open air area containing a berserk pack, computer area map and a small sniping window to facilitate killing the enemies who guard the red keycard.
Inside the room requiring the red keycard, cross the bridge between the two nukage ponds and open the left green skull panel to access a room full of health and armor bonuses and a chainsaw.
Inside the same red keycard door room, run up both staircases and hit both switches. After doing this, a green switch will be shown at the base of the eastern balcony. Flipping this switch causes one of the steps of the staircase leading to the opposite balcony to lower like a platform, showing a narrow sewage duct behind it. The duct leads to a lift with a rocket launcher, followed by a small room just behind the western balcony, full of ammo and a backpack. Just like secret #1, this secret is also quite tricky to acheive due to the short time the lift stays lowered before rising again.