The TMP novel mentions the Gibraltar dam, lowering the water level in the Mediterranean. Atr least at one time, Roddenberry saw Earth as engaging in geo-engineering, so they'd already have some practice with it. And the current would be rerouted by the mass of Atlantis - perhaps using solar mirrors to selectively heat sites in the ocean to induce the initial desired current? And perhaps some of the water was meant to be displaced into Death Valley, the sahara, or other inland seas? Or maybe they were going to beam up gigaliters to Luna, and this was a way to refill the bathtub a bit? If a permanent forcefield contained an atmosphere, and enough water and nitrogen was brought up, Luna could be terraformed into a shirt-sleeve environment. Although I think Mars and Venus would be better candidates - better able to hold on to the terraformed state without continuous power input at least. In in those cases, even with Trek tech, I'd use comets, instead, unless I needed a place to put excess seawater.