Since when were starship engines waterproof? And I doubt it would stay waterproof for long, especially being a ship constructed for the low pressure atmosphere of space, and then being put in high pressure under water... The more I look at these films the stupider they get.
But it's happened before in Trek. We've seen ships fly underwater, through liquid layers of gas giants, through space amoebas, through black holes and wormholes, through fluidic space... it's already pretty firmly established.
Also, this Enterprise was built in Riverside, Iowa