The novel opens with the family in the hold of a sailing ship, weathering a great storm. The ship's crew evacuate without them, and William and Elizabeth and their four children (Fritz, Ernest, Jack and Franz) are left to survive alone. As the ship tosses about, the father – William – prays that God will spare them.

The ship survives the night and the family finds themselves within sight of a tropical desert island. The next morning, they decide to get to the island they can see beyond the reef. With much effort, they construct a vessel out of tubs. After they fill the tubs with food and ammunition and all other articles of value they can safely carry, they row toward the island. Two dogs from the ship named Turk and Juno swim beside them. The ship's cargo of livestock (including a cow, a donkey, two goats, six sheep, a ram, a pig, chickens, ducks, geese, and pigeons), guns and powder, carpentry tools, books, a disassembled pinnace and provisions have survived.

Upon reaching the island, the family set up a makeshift camp. William knows that they must prepare for a long time on the island and his thoughts are as much on provisions for the future as for their immediate wants. William and his oldest son Fritz spend the next day exploring the island.

The family spends the next few days securing themselves against hunger. William and Fritz make several trips to the ship in their efforts to bring ashore everything useful from the vessel. The domesticated animals on the ship are towed back to the island. There is also a great store of firearms and ammunition, hammocks for sleeping, carpenter's tools, lumber, cooking utensils, silverware, and dishes. Initially they construct a treehouse, but as time passes (and after Elizabeth is injured climbing the stairs down from it), they settle in a more permanent dwelling in part of a cave. Fritz rescues a young Englishwoman (Jenny Montrose) shipwrecked elsewhere on their island.

The book covers more than ten years. William and older boys explore various environments and develop homes and gardens in various sites about the island. In the end, the father wonders if they will ever again see the rest of humanity. Eventually a British ship that is in search of Jenny Montrose anchors near the island and is discovered by the family. The captain is given the journal containing the story of their life on the island which is eventually published. Several members of the family choose to continue to live tranquilly on their island while several of them return to Europe with the British.