There is a specific order of tasks that you need to do in this level.
First you need to obtain the two chips that are in the first accessible area (near where the ammo teleports in). Setting the platforms from the control room is relatively simple in this case.
The second area is the large room with a low sewage level and a small control room. After saving here, fall into the water, and look behind the controls to find a switch to hit. This will raise the water level to allow access to the back of the room. In these passages, there's two switches that you have to hit. There's also a series of switches in a timed fashion that you need to hit to raise a bridge for later in the level.
The third area will open once you've done this second area. This leads to sewage filled areas. Jump in the sewage, and try using the little drain panels as doors. You'll find that you can get around the third area this way. Make sure you look at the map.. several times, you'll need to dive to get to an important switch.
The fourth area is the door well off the ground, and opens after you clear the third area. This area will require you to enter a coode. This code is in one of the terminals at area two, and you can see the code for the switches by switching to map view. If you enter the code wrong, you get switched. Nuf said.
Finally, after entering the code, and pressing the revealed switch, head to the center of the level, and hit the switches in the control room in that area, then make your way down to the floor of the pool, where your teleport awaits.
It's all really quite simple :-)
By the save term of area 3, there is a pool where some security drones emerge from. After dealing with those, dive down and grab the ammo at the base of the pool.