Freckles is a young man who has been raised since infancy in a Chicago orphanage. His one dream is to find a job, a place to belong and people who accept him despite his youth and the disability of having only one hand. He finds this place in the Limberlost Swamp, as a Limberlost guard of precious timber.

In the process, he discovers a love for the wilderness and animals he encounters every day on his rounds and a burning desire to learn about all the new birds and plants he sees on his rounds every day. He also finds and falls in love with a girl he calls the "Swamp Angel." This is the story of his plucky courage in sticking to his job in the swamp, and his adventures in learning about the natural world he finds himself in every day. He is befriended by the "Bird Woman" and with her help learns to love the Limberlost he has been hired to guard.