One can say that The Secret Garden is organized around the idea of secrets. Mary is a secret from her parents' associates; Colin is kept a secret by both his father and himself. Misselthwaite is full of hundreds of locked rooms which no one may enter; its servants are forbidden to speak of its history or of its current inhabitants. Colin keeps the portrait of his mother a secret from his servants, and, later, the secret of his newfound health from all but Mary, Dickon, Ben Weatherstaff, and Susan Sowerby. The secret of the garden itself is the most significant. One by one, each of the book's secrets are disclosed: disclosure is presented as an absolute good, for, in the economy of the novel, the content of a thing does not matter—only whether one thinks of it positively or negatively does. Thus the secret of Mistress Craven's death can be disclosed, provided one maintains that she isn't really dead at all; Colin and Mary can come to light, provided that they have become kind and healthy; the garden, too, may be unlocked, so long as it, too, is resurrected.
A number of striking similarities between Mary and Colin are immediately apparent: they are both ten years old; they have both passed sickly, neglected childhoods; both are unbelievably spoiled; and both have been looked after by retinues of servants who have been ordered to obey their every whim. Both children have parents that have denied their existence and hidden them away like secrets. No one ever sees Colin or Mary: the English soldiers who discover Mary in her parents' bungalow declare that they never knew that "that pretty woman" had had a child at all. Upon first seeing Colin, Mary exclaims, almost identically, "I never knew [Master Craven] had a child!" The garden has been closed for ten years; up to the moment that Colin and Mary each enter the garden, they too are closed off—they have loved no one, and have been utterly unloved. Because it has been so long since anyone has tended the garden, it is impossible to determine whether its flowers are dead or alive. Similarly, both Mary and Colin have had no one to care for them since their birth, and their skin has become either waxen or stony as a result. Both of these words ("waxen" and "stony") connote lifelessness. The awakening of the secret garden both parallels and is the cause of Colin and Mary's own rebirth.
Eden, also called Paradise, was the garden in which the first humans created by God (Adam and Eve) lived until the time of the Fall. The "Fall" refers to the moment that God cast Adam and Eve out of the Garden of Eden for tasting of the Tree of Knowledge. The secret garden is connected with Eden through Martha's story of the divine times had there by Master Craven and his wife before her quite literal "fall"—before, that is, she fell out of the rose-tree to her death. It is also similar to Eden insofar as it represents a Paradise of innocence and ideality for Mary and Dickon. As in Eden, they enjoy a uniquely close relationship with God (who occasionally is referred to as magic, and as "the Big Good Thing") when they are within its walls. Their work in the garden is compared to the work of "nest-building," which of course has certain marital implications—it is as though they too have become Adam and Eve. Furthermore, their seclusion in the secret garden conjures up that enjoyed by Master and Mistress Craven. This echo is strengthened by the fact that Mary bends down and kisses the newly opened crocuses, just as Mistress Craven kissed her roses. The Eden-like quality of their time alone together in the garden is only strengthened by the presence of Dickon's docile "creatures," which recall the animals created by the Christian God to keep the first people company. Dickon inspires "rapture" in Mary, which implies both ecstasy and "a mystical experience in which the spirit is exalted to the knowledge of divine things" (Merriam-Webster). Dickon's intimate connection with heavenly nature brings Mary nearer to divinity herself.