One, he doesn't have to go down to the Mariana trench.

He can make the gateways a couple of hundred feet below sea level, from the deck of a ship for ultimate comfort.

Once sea levels have dropped sufficiently, he can make new gateways at a lower level, and so repeat this rather effortless assault on the planet's climate.

Two, if he descends to the "Mariana trench" in a sphere of air, for example, he doesn't have to make the gateway right next to himself. Rand can make weaves up to 5 miles away, in FoH.

Even if Ishamael can only make a weave 1 mile away, that still gives him plenty of room to rise to the surface again without any danger.

And three, he can just make Deathgates that start close to the surface of the water and gradually move around, going deeper and deeper. That's the easiest solution of all. Only, he won't make them with random openings, he will make them all open into space.

There. That's three solutions in less than 3 minutes. I'm sure you could think of even more if you actually tried before just blasting away at the theory just because you felt like it.