I found that if you just jump straight into the water, chances are you’ll be killed or have little to no health left by the time you get rid of it.
The way I did it was to trigger the arrival of the helicopter, then rush back to the little warehouse. Thanks to the spare ammunition in there for the experimental laser gun thing, I just shot it with that until it flew away.
Simple, and especially useful for the fact that there are 2 health packs, and 2 charge stations in that particular warehouse.