Narrated in the first person by the novel’s protagonist, Rukmani, Nectar In A Sieve opens with Rukmani living with her son Selvam and Puli, a boy she adopted who has missing fingers. She hints that her husband has recently died.
Rukmani goes back in her memory to tell the story of her life. She was the youngest of four daughters. At twelve years old, she has an arranged marriage with Nathan, a tenant farmer seemingly in his late teens or early twenties. She moves to his village, taking up residency in the mud hut he has constructed and learning how to cultivate the rice paddy on the land they rent from a landlord they never meet. Rukmani is taught the ins and outs of being a farmer's wife by local women. She is excited to raise successful vegetable crops in addition to the rice.
Rukmani soon becomes pregnant with her first child, a daughter named Ira. She becomes depressed when six years pass without another child; in particular, Rukmani is sad not to have had any sons, as sons are more highly regarded in her culture. However, she appreciates that her husband doesn't shame her for not being able to conceive again. Kenny, a white doctor from England, gives Rukmani unspecified fertility treatments, and Rukmani proceeds to have five sons in five years. When a tannery is established in the village, Rukmani fears that it means the beginning of the end of their way of life. Others in the town welcome the industry and the money it will bring to the local economy.
When Ira turns fourteen, she is married to a man from a faraway village. Rukmani is sad to see her go. Ira's wedding is followed by monsoon weather that destroys the rice crop on which the family's survival depends. Others fare worse, being killed by lightning or drowned. The family scrapes together what they can, living off reserves until the next rice harvest. Meanwhile, more and more men from the village take jobs at the tannery, turning away from their families' subsistence farming traditions.
After five years of marriage, Ira's husband returns Ira to the family claiming she is barren. Ira is depressed, but knows his rejection was a long time coming. Arjun, Rukmani's eldest son, takes a job at the tannery, bringing his brother Thambi with him. Rukmani argues that they are not of the tanner's caste, but Arjun figures they need to make real money to support the household. Each son earns one rupee a day that they give to their mother. The entire family enjoys a higher standard of living and Rukmani stockpiles rice, lentils, and chillies.
Rukmani, without Nathan's knowledge, brings Ira for fertility treatments from Kenny. However, her ex-husband has already found a new wife. Rukmani worries Ira will turn out like Old Granny, a kind homeless woman who lives on the street in the village. Arjun and Thambi, meanwhile, organize a workers' strike at the tannery to demand higher wages. The owners force men back to work. Arjun and Thambi quit rather than demean themselves. They soon take jobs at a tea plantation in Ceylon. Rukmani learns from Kenny that he has a wife and child in England, but he has rejected the "chains" of married life and lives freely in India.
A drought destroys the rice crop. To pay their yearly rent, Rukmani and Nathan sell anything they can, barely scraping together half of what they owe. The family cultivates another crop, but starve as they live on paltry rice reserves until harvest time. Kunthi, Rukmani's nemesis, arrives one evening to say her husband has left her for another woman and her sons have their own wives to take care of. She demands Rukmani give her all the family's rice, threatening to tell Nathan about Rukmani going to Kenny for fertility help. Rukmani gives in to the extortion, reassuring herself that she has eight days' worth of rice hidden in a hole in the field. However, Kunthi has got to this reserve too, having extorted Nathan. Nathan confesses that he cheated on Rukmani, fathering both of Kunthi's sons. Rukmani admits to her fertility issues, and the couple puts their secrets behind them.
The family survives on scraps of food until they can finally harvest their grain. But before the harvest, Rukmani's youngest son, Kuti, dies of starvation. Rukmani learns that Ira has been engaging in sex work in the village to get enough money to buy milk to keep Kuti alive. Raja, another young son, dies when tannery guards attack him for trying to steal an animal skin.
Rukmani's son Selvam, among the most educated of her children, gives up trying to farm when Kenny offers to train him to be his medical assistant. Together, the men oversee the construction of a village hospital for which Kenny fundraises back in England. The project will take seven years to finish.
Ira becomes pregnant from an unknown man and gives birth to Sacrabani, a boy born with albinism. The condition becomes a novelty among the locals, who have a superstitious prejudice against his difference. Ira accepts the boy for who he is, and accepts that she will raise him without a father. Selvam also treats Sacrabani as inherently lovable and scolds the adults for their prejudice.
After thirty years of working the land, Rukmani and Nathan learn that their rented farmland has been sold to the tannery owners. Sivaji, the middleman, gives them two weeks to leave. Too old to lease other land, Nathan and Rukmani reason that they should move to the city where their son Murugan works as a servant. Rukmani does not look forward to living in her daughter-in-law's household but accepts her fate.
The couple makes the journey by bullock cart only to discover that Murugan has abandoned his wife and child, drawn away from family life by the allures of women and gambling. In the city with no money or possessions, Rukmani and Nathan sleep at a temple that gives away one free meal a day. Puli, a charming and wily homeless orphan who has lost his fingers to disease, befriends them. He accompanies them to a rock quarry where they can break rocks all day to earn money to travel back to their village. When they've almost raised enough, Nathan comes down with a fever. He continues breaking rocks despite his illness and the monsoon rains. Eventually, however, he collapses in mud, dying that night while Rukmani kneels next to him.
The novel ends with Rukmani returning to the village. She has brought Puli, saying she has adopted him. Selvam assures his mother that they will manage. She says that Nathan's death was gentle and that she will tell him about it later.
