The narrative begins in the grimy industrial North of England, where young Tom suffers under his brutal master, Grimes. After wandering into the grand Harthover Place to sweep its chimneys, Tom accidentally startles a young girl named Ellie and flees in shame, diving into a clear limestone stream to wash his soot-stained skin. There, transformed by mysterious river fairies into a water-baby, he embarks on an aquatic adventure that spans the English countryside, the deep sea, and mystical realms. Throughout his underwater existence, Tom encounters various creatures—caddis-flies, dragon-flies, otters, and salmon—who teach him the consequences of selfishness, cruelty, and ignorance.
He learns to navigate the moral universe governed by stern yet benevolent fairies, Mrs. Bedonebyasyoudid and Mrs. Doasyouwouldbedoneby, who mete out strict lessons on behavior.
As Tom grows more compassionate and sheds his rough habits, he yearns to reunite with Ellie and seek redemption for his past. His quest ultimately leads him through strange lands and past magical barriers, culminating in a transformative journey toward self-discovery and ultimate maturity in the mythical St. Brandan's Isle.