what if the water was the same as the cloud cover. you know how when u fly above 20k theres that blanket of thin cloud. what if the water was designed the same way, only the layer was on the deck and they could program the subs with "distinct flying" characteristics which are able to move below sea level (which would be similar to the cloud cover it would just be a thicker blue layer). at that they would put in that barrier that instantly towers any plane from crossing below the water layer.
im no computer guy this is simply my .02 cents hopefully this paints a decent picture and contributes to the ideas.