A Long Walk to Water begins as two stories, told in alternating sections, about two eleven-year-olds in Sudan, a girl in 2008 and a boy. The girl, Nya, is fetching water from a pond that is two hours' walk from her home: she makes two trips to the pond every day. The boy, Salva, becomes one of the lost boys of Sudan, refugees who cover the African continent on foot as they search for their families and for a safe place to stay.

When a young man returns to his village in the Sudan after many years studying in Europe, he finds that among the familiar faces there is now a stranger - the enigmatic Mustafa Sa'eed. As the two become friends, Mustafa tells the younger man the disturbing story of his own life in London after the First World War.