The robin is symbolic of Mary's budding relationship with the natural world. By witnessing the way people like Dickon or Ben Weatherstaff interact with animals, Mary comes to learn how animals are living beings with a spirit not so different from her own. This is also emphasized when the narrative is momentarily told from the perspective of the robin, showing the reader how the birds that inhabit the gardens are a vital and conscious aspect of the ecosystem, with hopes and fears of their own.

The Secret Garden is the central symbol of the story, representing revitalization and how even those things that appear lifeless may regain their health with the proper nurturance. It is Mary's determination to see the garden bloom that allows it to transform from a shameful secret into a meeting ground for the characters to connect and enjoy the beauty of nature.

Through the guidance of Dickon, Mary learns about the diversity of plants and how to care for them. As Mary works on cultivating the garden, she simultaneously grows as a person and becomes more mature and happy. Similarly, Colin is replenished and brought out of sickness through his encounter with the magical garden.

Though the garden was left to wither by Mr. Craven, not all is lost; the rose plants, the favorite flower of Mrs. Craven, are still holding on to life. Thus this is meant to show how despite the depths of human despair, the will of nature to thrive is much stronger.