The boss battle in the Flooded City is an almost entirely aerial fight. This is the same fight where you earn Ruler of the Deep once you complete it. However, if you're fairly decent at the aerial combat, you should get this trophy during the first section of the fight.
You don't need to kill all of the enemies to earn this trophy, and over the course of the fight there will be more than enough that unless you're deliberately trying not to kill them, this trophy is basically automatic.
If you're like me, you may find the start of the fight is different from previous aerial segments - if you've been using Pod C instead of Pod A, your normal automatic gun will be gone. Just switch Pods to switch weapons back to the gun.