''The Message in the Sand Dunes'' follows 16-year-old amateur sleuth Kay Tracey and her closest friends, twins Betty and Wilma Worth. Kay foils a robbery at the home of the eccentric Crowley sisters by cleverly tapping on a window pane to scare the burglars away. The event sparks a larger mystery regarding what valuable items are hidden inside the Crowley house.

Kay searches for clues across a desolate stretch of sand dunes, uncovering secrets involving a missing young couple and a man named Ben Wheeler. Adding to the action, Kay pulls off a daring, coolheaded rescue of a famous airplane pilot who crashed at sea.