In Deep River, four Japanese people of different backgrounds and different sorrows converge at the holy Ganges River in India, on their own personal journeys to reconcile themselves with their pasts. Isobe is a taciturn man left desolate by the death of his wife and searching for her reincarnated soul. Kiguchi, a former Japanese soldier who endured torturous hunger and illness in Burma during World War II, mourns the wartime friend who saved his life, but suffered and died because of his guilt. Numada, a children's author whose only true friends have been animals and birds, seeks to repay the help of a myna bird. Mitsuko, an atheistic woman whose life has been without love, seeks her college lover, a failed Catholic priest working among the impoverished. All four find some solace in the Ganges.

As the novel begins, Isobe finds out his wife is dying from cancer. He does not tell her the truth, but as she sickens, she knows she is dying. Right before his wife dies, she tells Isobe that she knows she will be reincarnated and begs him to search for her. Isobe cannot forget Keiko's request and writes to researchers studying reincarnation. He learns of a little girl in India who claims to have been Japanese in a past life. Mitsuko, who nursed Isobe's wife as a volunteer also happens to be on Isobe's tour of India. Mitsuko is divorced, and has lived a loveless life. She has heard that the religious young man she seduced in college, Ōtsu, is in India. Mitsuko visited Ōtsu once before, during her honeymoon in France, when he was studying at a seminary, and they talked about his idea of his "Onion," a God of both suffering and love.

Numada, a children's author, is also on the tour. He has recovered from a near-fatal bout of tuberculosis, and a myna bird was his companion during his illness. The bird died during Numada's last operation, and Numada feels the bird died in his place. Kiguchi, another traveler, was a soldier during World War II in Burma. In Burma, he contracts malaria, and his friend Tsukada refuses to leave him behind. Later, Kiguchi learns that Tsukada ate the flesh of a dead soldier to survive and save his friend. Tsukada drinks himself to death because of his guilt over the act.

The tourists arrive at the River Ganges, where Mitsuko, Isobe, Numada, and Kiguchi all stay behind. Kiguchi is ill, and Mitsuko stays to care for him. Isobe searches for his reincarnated wife, but fails to find her. Instead, he finds only memories of their life together. Numada frees a myna bird, in repayment to the bird who saved him. Kiguchi reads a prayer for dead soldiers over the sacred River Ganges. Mitsuko finds Ōtsu, who is working among the poor and dying Hindus, carrying the impoverished to the Ganges so their ashes can be scattered in the sacred river. The traveler's stay is complicated by the assassination of Indira Gandhi, and the following unrest. Ōtsu, who has given his life over to the Onion, sacrifices himself by stopping a group of men from attacking one of the Japanese tourists, and being beaten to near death. As Mitsuko and the other tourists finally leave, she learns that Ōtsu is in critical condition and has taken a turn for the worse.