The water might have gone to the natural places where it should go: oceans, rivers... The harbor shown in the movie might have been an artificial one, higher than the planetary zero level of water and kept wet only via dams and water gates. No humans to operate them meant the water slowly went away and the ships slowly sat in the sand. Actually, there is a scene where some oil ships fell down like dominoes after one of them is hit by Eve. That might suggest that the ships were sitting in a very fragile equilibrium, compatible with the theory of them slowly going down and resting on the bottom of the bay.