The titular Freckles is an orphan missing his right hand who runs away from the future the orphanage set for him in favor of making his own. After finding his way to the Limberlost, an area of swamp land in Indiana, he finds a job, conducts himself with honor, and finds love, family, and joy. The swamp, however, is not without its dangers, and he must stay vigilant to protect those who are dear to him.

Gene Stratton-Porter had great success with Freckles and its follow up, A Girl of the Limberlost . Freckles itself would go on to see five separate film adaptations as well as an adaptation into a Japanese manga series, Sobakasu no Shōnen .