If there's a monolith on a square next to the coast, send a seaformer to a sea square next to the monolith and lower the elevation. It'll cost 144 EU. The square with the monolith becomes a sea square but the monolith doesn't go away! You can run ships and Isles of the Deep to the monolith and get an upgrade and/or repair damage. If you have units on the ship/Isle, select them and they will be upgraded/repaired as well. Like regular monoliths, a ship/Isle only gets one upgrade.