The book The Light Between Oceans, on which this movie is based, contains three coincidental links to previous films of Michael Fassbender. First, his character Tom travels on the ship SS Prometheus: Fassbender starred as android David in Prometheus (2012). Second, Tom's wife, Isabel, is given a gramophone record, Bach's Goldberg Variations, as a gift: this piece of music was the soundtrack to the jogging scene in Fassbender's film Shame (2011). Finally, in Frank (2014), towards the end of the movie, Fassbender's Frank walks into a bar, where Maggie Gyllenhaal is singing the song "I Want to Marry a Lighthouse Keeper". Fassbender's character in The Light Between Oceans, Tom, is a lighthouse keeper.
The book and movie's plots are very similar to the screenplay of the film The Rootcutter (later retitled A Tale of Two Humans), written by Joseph Nobile a decade before the book The Light Between Oceans was published. In Nobile's script, a couple living on a remote Irish island have had three stillborn babies. They're about to give up hope when the husband finds a boat adrift with a crying baby and a dead adult inside. After bringing the baby home and debating whether to tell the authorities, they agree to raise the baby as their own, with eventual tragic results. Nobile's film is in development.
Some of the films key scenes were shot in Port Chalmers just outside Dunedin. The bulk of the film is set at a Lighthouse at Cape Campbell in Marlborough, New Zealand. The cast and crew lived there for 5 and a half weeks.