Inspired by the author's own experiences and stories passed down, Willie Sawgrass takes place in the wilderness of Southwest Florida in the early 1900s, when the cattle and fishing industries were strong but rum running was more lucrative. Willie isn't sure how old he is when his ignorant and abusive Pa sends him away to live with a young Miccosukee woman and her son, Nakee.

Willie and Nakee form a tight bond and share many adventures, like fighting an alligator and confronting a family of skunks. They eventually get stranded at sea in a dugout canoe, only to be rescued by the well-educated Captain O'Keef. He takes the boys aboard the Bonnie Sue as extra deckhands on the big fishing schooner and teaches them the importance of reading and writing.

Just as the boys are feeling comfortable in their home on the Bonnie Sue, everything changes when they rescue two men and some cattle from a sinking ship, bringing a mystery into their young lives. Willie and Nakee find themselves amid shady characters but manage to solve a mystery and get their revenge in the end.