Lily, a fourteen-year-old white girl, lives alone with her father, a peach farmer, in Sylvan, South Carolina. As the novel opens, she lies in bed, waiting for the bees that live in the walls of her bedroom to emerge and fly around, as they do most nights. T. Ray, her father, is abusive and does not believe her story about the bees. Her nanny and housekeeper, Rosaleen, believes Lily but also thinks Lily is foolish for trying to collect the bees in a jar. Lily recalls her very last memory of her mother, Deborah, who died when Lily was a small child. Lily thinks that she played a horrible part in Deborah’s death. In a flashback, readers learn that T. Ray told Lily that she accidentally shot Deborah while Deborah and T. Ray were fighting one day. The next morning, Lily accompanies Rosaleen into town, where Rosaleen intends to register to vote. Instead, a group of racists harass Rosaleen, who winds up getting arrested for affronting them. T. Ray picks up Lily at the prison and tells her that the men who accosted Rosaleen will most likely kill her. This news understandably frightens Lily, particularly as Rosaleen is the only person in her life who truly loves Lily. At home, T. Ray tells Lily that on the day she died Deborah had returned home to pick up just her clothes, intending to leave Lily behind. Lily notices that the bees have escaped from the jar she put them in, which leads her to have an epiphany: she needs to run away.
Lily finds Rosaleen at the hospital, where Rosaleen has been taken after being beaten up by the arresting police officers. Together, Lily and Rosaleen hitchhike toward a town (Tiburon, S.C.) that Lily has found written on the back of a picture of a Black Mary that once belonged to her mother. On the way, Lily feels free, as if a new life has begun for her. Rosaleen feels annoyed that Lily has broken the law only to head toward a town loosely associated with her deceased mother. In Tiburon, Lily learns that the Black Mary picture comes from the label of a honey maker in town. Searching for this honey maker, she comes across the bright pink house of August Boatwright and her sisters. August invites Lily and Rosaleen to stay, although Lily makes up a false story to explain their needs. August decides that Rosaleen will help her sister May Boatwright around the house and Lily will learn beekeeping.
Soon Lily and Rosaleen become members of the community centered around the Boatwright house: a close-knit group of African Americans, mostly women, who call themselves the “Daughters of Mary” and worship a three-foot-tall statue of a Black Mary. Lily meets the honey farm helper, Zach, a handsome, intelligent, African American boy on whom she develops a crush. He develops feelings for her as well and buys Lily a notebook in which she can write stories. Lily grows closer and closer to August, beginning to love her and to find in her a surrogate mother. August urges her to open up about whatever led Lily to end up in Tiburon, but Lily worries that she will be sent back to Sylvan if the truth comes out. Meanwhile, Lily also learns how to care for bees and to understand her own ingrained prejudices. She visits a white lawyer in town who is helping Zach fulfill his dream of becoming a lawyer. At the lawyer’s office, she breaks down and calls her father. T. Ray is angry and indignant. The experience makes her miss her mother but also reaffirms her decision to run away.
On a very hot day, Lily asks May if she ever knew anyone named Deborah Fontanel and learns that she has. With this, Lily receives absolute confirmation that her mother once spent time at the Boatwright house. Lily is simultaneously eager to find out more and anxious about exposing her true identity as Deborah’s daughter. On her way to talk to August, Lily decides instead to ride with Zach into town to buy pieces for the car. There, Zach is amongst a group of Black boys that assault a white man, and the entire group gets taken to jail. When Lily returns home, Clayton, the lawyer, has arrived to tell the Boatwrights that Zach has been arrested. They decide to hide the news from May, the most sensitive sister, because they know how upset she’d be. But May finds out and leaves the house alone. She commits suicide by drowning herself in the river. The next week is taken up with mourning and a funeral. Once another boy confesses, Zach is let out of jail, unpunished. Lily fails to find a chance to speak to August.
One morning, Lily wakes to find that it is Mary Day and that the mourning is over. A two-day celebration begins. During it, Lily finds herself alone with Zach. He kisses her, and they vow to try to be together in the future, though they both recognize that their union is, at present, impossible. Lily then goes to August’s room to wait for her. When August arrives, Lily tells her the truth of her life, of how she ended up in Tiburon and of how she killed her mother. August admits that she has known Lily’s true identity all along and corroborates Lily’s worst fear: that Deborah had already left her when she returned home and was shot to death. Deborah had gone to the house only to pick up her clothes. Feeling betrayed and upset, Lily begins to mourn for her mother. Days later, after she has recovered from her grief, her father arrives at the Boatwright house. Though T. Ray is angry and violent, Lily finally has the strength to confront him about the past and to call him “Daddy.” August convinces him to let Lily stay in Tiburon.
As T. Ray leaves, Lily asks him if she really killed her mother. He reports that she did. However, Lily has come to realize that he, just like her mother, is a flawed and complex human. In a way, she forgives him, but she nevertheless feels happy to continue living at the Boatwright house. In the fall, she returns to school, which she attends with Zach and where she makes other friends. August and her community become Lily’s new family, and, at long last, Lily develops into a loved and loving person.