A little to the right from the gate there's a box titled "Authorized Personnel" - open it up, by using the interaction button. A little puzzle awaits you here. To open the gate, you must grab the round switch and:
- Turn it clockwise, until it "clicks"
- Pull it towards yourself
- Turn it counter-clockwise, again, until it "clicks"
- Push it inside
Afterwards, all there's left to do is to pull the lever down, and after a short while the gate will open. Get inside and use your Omnitool to activate the switch. The water will be pulled away and the further part of the passageway will be available.