After you get into the waterfilled part of the level, familiarize yourself with the layout. Specifically, note that there is a stairway that gets you out of the water, and to two terminals. The second term requires you to drop down, then turn a corner to get to, but this term will teleport you to a different part of the level, where you can get the chip needed.
Once you've gotten the chip and exited the chip room via the stairs, you can jump down to the insertion point just below you.
With the chip in place, the bottom of the tower farthest from your current position will open. This opens onto an elevator that gets you to the a destroyable switch. This opens the next tower down the line, which you can repeat over and over again.
Upon destroying the last switch in the last tower, a door near the first terminal will open, getting you to the last part of the level.
When you exit the first room and overlook the waterfilled area, there are several ledges on the right, which you can jump to, and leads to a secret room with lots of ammo. You can exit this secret area via a hallway that gets you into the main level, but there are lots of nasties in this path, but you may just want to open the door and jump into the water instead once you've gotten your goodies.