Filming took place in 2006 in New Zealand, Scotland and at Miramar Studios in Wellington. Most of the film was shot in New Zealand, with Queenstown's Lake Wakatipu doubling for a Scottish Loch. The filmmakers found that some of the landscape and geography there was similar to Scotland. However Russell said, "There was no way I was going to make a movie about the Loch Ness monster and not shoot at least part of it in Scotland."
The scenes in and around the MacMorrow family's house were shot on the 100-year-old Ardkinglas Estate on the shores of Loch Fyne in Scotland. The owners of the estate continued to live in the house while the crew was filming there.