The book alternates between two storylines: one beginning in 1985 and revolving around Salva Dut, an eleven-year-old boy living in the South Sudanese village of Loun-Ariik; the other beginning in 2008 and revolving around a young South Sudanese girl named Nya.
On day in 1985, Salva is sitting in school when he hears the sound of gunfire. There’s a violent civil war going on in his country, and Salva’s teacher yells for everyone to run away from their village as fast as possible. In the chaos, Salva is separated from his parents and siblings. He spends a few nights staying with an elderly woman in her barn, but the woman eventually tells Salva that he’ll need to keep moving, since there’s no more food or water. Salva joins up with a large group of people from his village, and the group begins to wander across Sudan in the hopes of finding a safe refugee camp.
After weeks of wandering across Sudan, Salva befriends another boy in the group, whose name is Marial. A few weeks later, Salva is overjoyed to be reunited with his Uncle Jewiir, who used to be a soldier. Jewiir, recognizing that Salva’s parents are nowhere to be found (and thinking they are likely dead), promises to take care of Salva. He becomes the de facto leader of the group, due to his gun and his military training.
One night, Salva wakes up to find that Marial has disappeared. Jewiir guesses that Marial has probably been eaten by a lion.
The group of refugees finally reaches the Nile River. By building boats out of reeds, everyone is able to cross to the middle of the river, where there is an island of fishermen. On the island, Salva enjoys more food than he’s had in months. The group then proceeds onward to the other side of the river, in Ethiopia.
The next stage of Salva’s journey is the hardest of all. The group must cross the Akobo desert—a journey that will take them three days. Midway through the long march, the group encounters a group of men who are near death from dehydration. To Salva’s amazement, some of the adults in the group give their water to the men, thereby saving their lives.
When the group is almost out of the Akobo desert, it crosses paths with a group of soldiers. The soldiers steal the groups’ food, supplies, and clothes, and murder Uncle Jewiir in front of Salva. Salva is devastated by his uncle’s death, but he promises himself that he’ll keep on moving—just as Jewiir would have wanted him to do.
Salva and the remaining members of the group march into Ethiopia, where they come to a refugee camp. Salva stays in the camp for six years, at which point the Ethiopian government collapses, and the new government forces refugees out of the country. Salva has no choice but to migrate into neighboring Kenya—a dangerous journey which takes a year and a half, during which time Salva emerges as the leader of his group of more than one thousand young boys. Salva leads the group safely to Kenya, where he stays in two different refugee camps until he’s in his mid-twenties. Salva is often lonely, but he befriends a foreign aid worker named Michael, who teaches him how to speak and write English.
One day, it is announced that a few thousand Sudanese refugees will be adopted by American families. To Salva’s surprise, he is placed on the list of boys that will be adopted, and is flown to Rochester, New York, where he lives with an American couple named Chris and Louise.
In 2003, Salva is about to start college. He receives a surprising email from a cousin, whom he’s never met before. The email explains that Salva’s father, Mawien Dut, is still alive, and is staying in a U.N. hospital in Sudan. Overjoyed, Salva arranges to travel back to Sudan. There, he has a tearful reunion with his father, and learns that his mother and sisters are alive, although two of his brothers died in the civil war. Salva is unable to return to his village, since the risk of being forced to fight in the war is too high. However, he vows to return to Sudan one day.
After returning to America, Salva is determined to use his advantages to help the suffering people of Sudan. With the help of Chris and Louise’s friend Scott, Salva founds a nonprofit organization with the mission of building wells in impoverished Sudanese villages.
In the book’s second storyline, which takes place between 2008 and 2009, Nya spends her days fetching water for her family, which means repeatedly walking to and from the large pond located miles away from her family’s village. Walking so much is physically exhausting for Nya, but her family depends on her, as many families in the village depend on their daughters, to bring them water while they complete other vital tasks. Furthermore, the water from the pond is not clean, which is a constant source of illness for the people who must drink it.
One day, mysterious men arrive in Nya’s village and begin speaking with the village chief. The villagers begin clearing the land in the center of the village for construction—although Nya doesn’t understand exactly what the men are building. As the months go by, Nya learns that they’re building a well that will provide clean water to the area.
By the end of 2009, the well is completed. Nya is delighted to learn that she will no longer have to march miles every day just to get clean water—since, from now on, there will be clean water available to her in the center of the village. Nya learns that there will also be a schoolhouse built, where she will able to learn how to read and write, an option that was previously unavailable to most South Sudanese girls, who were expected to spend their time fetching water.
As the book comes to an end, Nya introduces herself to the man responsible for designing the well in her village, and thanks him. He smiles and introduces himself as Salva.