[4] The story is told from the viewpoint of fourteen-year-old Charlie Fox and centers on his father, Allie, a brilliant inventor ("with nine patents, six pending") who becomes increasingly critical of consumerism in the United States, education and culture.

Allie decides to move his family from Hatfield, Massachusetts, to escape the influence of the United States and the world war he fears is imminent, to enjoy a simpler life in La Mosquitia on the eponymous Mosquito Coast of Honduras.

During a violent storm, Allie repairs a bilge pump and has several run-ins with Reverend Spellgood who is traveling with his family to his mission in Honduras.

He transports the ice it produces farther up the river to isolated tribesmen, only to find to his disgust that missionaries have already reached them and 'corrupted' them to the ways of the West.

He tricks them and locks them in 'Fat Boy' intending to freeze them to death, but their gunfire causes an explosion which kills the three gunmen, destroys Jeronimo and pollutes the river.

Escaping the explosion, Allie leads his family and Mr. Haddy through the jungle to Sico River, determined to move even further from civilization, and become less dependent on technology.

On arrival they convert an abandoned dugout into a hut, beachcombing for materials (including an outboard motor which Allie repairs) and planting crops on the shore, achieving total self-sufficiency.

"[5] Kirkus Reviews criticized the novel's plausibility, pacing and thin characterizations, but goes on to say that "though the presentation of the serious ideas here is more noisy and colorful than thoughtful, the storytelling itself—full of clever descriptive writing and inventive action—sustains the entertainment mightily"[6] The novel was first adapted into a 1986 film starring Harrison Ford, Helen Mirren and River Phoenix.