Another vague one, I’m sorry!
I remember one scene only – of a boy diving to retrieve something from a spacecraft which is underwater. He may have entered through the roof, or possibly through a damaged section. He may have had a large conch shell or similar.
I don’t recall if the boy was human or actually alien masquerading as human but I’m inclined to think the latter.
I don’t think it’s Flight Of The Navigator (since the craft there is captured) or either of the Cocoon films.