suuuure, its been a few years, but basically the aliens have been here for thousands of years. water is fairly irrelevant to them, as its the pressure they are after.
the aliens can manipulate their environment at the molecular level so can easily create oxygen wherever they want. they can trivially read humans minds. they basically dont care about the advance of the human race until one day one of their peeps hits a satellite in space, crashes into the ocean and causes a united states nuclear submarine to crash, killing all crew.
the events of the movie pick up here. the aliens are remorseful about the submarine, while investigating they cause the events in the movie...towards then end a nuclear weapon lands on top of them. they of course already understand that the main character sacrifices himself to save them, whom they know he is unfamiliar with. he (and the memories of all the humans they have scanned) convinces them humans are not all bad.
the aliens realize they can no longer ignore the humans, and so expose themselves, bringing their ship out of the water. I believe in the book they also generate a giant tsunami wave out across the whole earth that halts in mid air right at the shores of the worlds beaches.
this is to get our attention.... we are not alone, or even in charge, anymore.