Mary Lennox is a sour-faced, sickly British girl about nine years old, who is living in India. When her parents die during a cholera outbreak, she moves to Yorkshire, England, to live with her uncle, Mr. Craven, in Misselthwaite Manor. Forced to go outside to amuse herself, she finds the key to a locked garden and becomes obsessed with restoring it. It becomes her secret place. Together with Dickon, the brother of Martha, one of the manor's servants, she tends its plants so she can make the long-abandoned garden come alive again. As she does so, she begins a process that heals her physically, mentally, and spiritually. As a result, she becomes a happy and empathetic child. Mary also discovers a hidden inhabitant in the manor, Colin, a sickly, self-absorbed, spoiled, invalid who is Mr. Craven's son, her cousin. She befriends him, and he joins her in the secret garden, where he undergoes his own personal journey of healing, with her support.
Colin is a young boy whose mother died shortly after he was born, and whose father has rejected him out of grief. As a result, Colin believes he will become a hunchback and die while still young. This belief has turned him into an invalid with a weak back and legs, who is often sickly and does not walk. He lives in a set of luxurious rooms in Misselthwaite Manor and has only limited interactions with other people. Mary says he acts like an Indian Rajah, a boy prince, because he orders everyone around in an imperious way. After Mary discovers Colin, they become friends. She visits him often, and they read and talk. Mary and Dickon persuade Colin to go outside, and he joins them in the secret garden, which changes his life. There, he learns to stand, walk, and run, becoming healthier, both physically and mentally. When his father returns from a long trip, Colin reveals his newfound health and his desire to be an athlete. The father and son mend their relationship.
Mr. Craven takes Mary into his home, Misselthwaite Manor, in Yorkshire after her parents die. A semi-recluse, he continues to mourn the accidental death of his wife a decade before. He hates to see his son, Colin, because Colin is alive while his mother is not, and he avoids the boy as much as possible. He wants nothing to do with Mary, either, other than to make sure her physical needs are met. Unable to bear the sight of his sickly son, he leaves the manor and travels around Europe for many months. During his travels he has a mystical experience in which his wife appears to him in a dream. It makes him feel as if he is coming alive again. Like Mary and Colin, he undergoes a personal transformation, returning home determined to repair his relationship with his son.
Although she dies before the events in the novel take place, Mrs. Craven's death has a significant effect on her son, her husband, and Misselthwaite Manor. A sweet, kind woman who created a garden where she and her husband loved to spend time, she died 10 years earlier after a tree branch she was sitting on broke and fell; she died the next day. Colin's only knowledge of her is a curtained picture that hangs in his room. Her death sends Mr. Craven into a spiral of grief. As a result, he ignores his young son and fails to give him the parental attention he needs. Colin sometimes hates his mother for dying and thinks that if she had lived his father would not have rejected him. The manor becomes a cold place devoid of love and human interaction after her death, and Mr. Craven locks up her beloved garden. Nonetheless, Mrs. Craven reaches out to her family from beyond the grave. Mrs. Sowerby believes she is present in the garden and watches over Colin. She appears in a dream to her husband and urges him to come to the garden. She transmits her love to her son and husband in this manner to help them heal themselves and heal their relationship.
Mrs. Sowerby barely appears as an actual character throughout most of the novel. Instead, other characters talk about her, referring to her words of wisdom and talent for nurturing children, making her the novel's idealized mother figure. She is first mentioned by her daughter, Martha, who shares with Mary her mother's wisdom about the benefits of fresh air and exercise. Dickon shares his mother's wisdom throughout the novel as well, thus passing on her nurturing to Mary and Colin. Mrs. Sowerby sends Mary a jump rope just after the child arrives at the manor, an important gift that touches Mary and encourages her to exercise outdoors. She also intervenes in their lives by talking with Mr. Craven about Mary's care and sending a letter to him urging him to return home. She finally meets Mary and Colin once they are both healed, and they show her around the garden.
Ben Weatherstaff becomes one of Mary's earliest friends and talks to her about friendship, loneliness, plants, and the robin. Like Mary, he is standoffish and sour, and not an easy person to get along with. After he discovers that Mary, Colin, and Dickon have found and restored the secret garden, he forges a closer relationship with them. Like Colin and Mary, he transforms from a gruff, solitary man who has few close relationships to one who is caring and content.
Dickon is an animal charmer with great empathy. He knows how to communicate with animals, which he often rescues and nurses back to health. He is equally adept at putting people at ease. Dickon's friendship is key to helping Mary and Colin heal and become healthy individuals as he shares with them his friendship and the wisdom of his mother, Mrs. Sowerby. Dickon responds to Mary's needs intuitively and gains her trust. He buys seeds and gardening tools for Mary and then agrees to help her tend the garden and make it come alive again. Dickon nurtures Colin the same way by helping him gain confidence in himself as they work in the garden together.