Tom Warder, born on the Pine Ridge Reservation, works at the LaCreek refuge, which hosts the nation's last remaining trumpeter swans. The refuge manager assigns Tom, who owns land adjacent to the refuge, to be the swans' day-to-day caretaker. Tom's land isn't productive enough to make a sole living from it, so he leases grazing rights to white rancher Bart Johnson.

Bart has fallen into debt and is unable to pay the lease he owes not only on Tom's land but also on land he leases from other Native landowners. As he sinks into debt his wife, Betty, becomes more extravagant and resistant to pleas for economy, while their son, Brian, becomes fascinated with hunting and begins stalking the trumpeter swans for the thrill of killing one. As his finances and his family fall apart, Bart takes to drinking. Meanwhile Tom's wife, Anna, and three daughters struggle to make ends meet, though their eldest daughter, Bit, who often assists her father in the care of the swans, is bright and determined to become something. Where Bit is the hope of her family, Brian is the disaster of his.

An Endangered Species is a tale of two families, each with their own strengths and weaknesses, bound to circumstances largely beyond their control, and struggling to survive on the upper Great Plains during the 1960s.