There's a movie that used to be on HBO in the late 70's/early 80's about a girl (& her brother I think) and they were stuck in a library or a museum or a castle all night. I seem to remember something about some kind of underwater adventure in part of it, almost like Bedknobs and Broomsticks, but a much darker feel and I'm not sure if there was animation in the film. I wish I had more details, but I rememeber loving this movie, but can only remember bits and pieces of it.

This may be extremely far off, but could it be From the Mixed-up Files of Mrs. Basil E. Frankweiler: YouTube - Ingrid Bergman in From the Mixed-Up Files of Mrs. Basil E. Frankweiler Trailer (aka The Hideaways)

It is about two children who run away from home, hide out in a museum and try to solve a mystery. I don't remember an underwater adventure, though. Unless you count bathing in a fountain.