From what i've seen so far (in trailers and news sources), is that they hide the Enterprise under the water surface, and Kirk and Bones are disguised in heavy clothing. Both of which, to prevent the indigenous population from realizing it's an alien species.
What I don't know, is why the Enterprise is hiding under water. If it's a pre-warp civilization, it's not likely they have any form of surveillance satellite system. The Enterprise could remain in orbit. HOWEVER... If there is something in the atmosphere preventing the transporter from being used, and if there is a major reason to bring the ship into the atmosphere, I could see them hiding it under water. Not hiding very well if they "land" it.