Oh, OK, quick SGA primer: Atlantis in this case is basically kind of a huge self-contained city that can and has traveled from the bottom of an ocean to the surface and even through space. Atlantis was built by the same race that built the Stargates, the Ancients, and most of this happened millions of years ago. When the Ancients left Atlantis behind they also left a trace of their genetic material (honestly, I'm unclear how this happened, if it was seeded purposefully or something else), and this specific gene is what allows the control of Ancient technology - it responds in a way that at times is virtually telepathic, but only to someone possessing the gene.

Very often a certain amount of training is needed to actually control this technology with any kind of accuracy, which can result in some wild results at first. Ray's panic manifested as the city sealing itself up and shutting down, therefore shutting down any possibility of him having to deal with the ocean.

How's that?