After many years, dragons have hatched again outside the ancient city of Cassarick. But something is wrong with the creatures; each is inferior or weak in some way, and many die. Tending these stunted dragons has left the people of the surrounding area weary. The Traders Council, the city's leadership, fears that if the Rain Wilders stop providing for the young dragons, the hungry and neglected creatures will rampage and destroy Cassarick. To avert catastrophe, the council rules to relocate the young dragons to "a better location" up river, and residents are recruited to escort the valuable yet fearsome creatures on the arduous journey. Among them are Thymara, an unschooled Rain Wilds girl of sixteen, and Alise, a wealthy, educated, and deeply unsatisfied Bingtown Trader's wife.

Witnessed from the viewpoints of these two very different women, Dragon Keeper tells the story of this disparate band of humans and dragons as they make their way along the toxic and inhospitable Rain Wild River in search of their new home—-the ancient, long-lost city of Kelsingra.