Although the book addresses many different issues—poverty, alcoholism, lying, etc.—its main theme is the need for tenacity: the determination to rise above difficult circumstances. Although there are naturalistic elements in the book, it is not fundamentally naturalistic. The Nolans are financially restricted by poverty yet find ways to enjoy life and satisfy their needs and wants. For example, Francie can become intoxicated just by looking at flowers. Like the Tree of Heaven, Brooklyn's inhabitants fight for the sun and air necessary to their survival.
Idealism and pragmatism are weighed and both found necessary to survival in Brooklyn. Johnny lies about his family's address in order to enable Francie to attend a better school, presenting Francie with opportunities that might not have been available to her otherwise. Sissy helps Johnny recover from alcoholic withdrawals by appealing to his libido, helping Katie and Johnny to stay together despite Johnny's disease. Katie explains love and sexuality to Francie from two somewhat clashing points of view: as a mother and as a woman. The book revises traditional notions of right and wrong and suggests pointedly that extreme poverty changes the criteria on which such notions, and those who embrace them, should be judged.
Gender roles are more fluid in A Tree than in previous novels about young people. Katie's hands grow rough as she performs physical labor while Johnny's hands remain smooth and he wears expensive clothing. Francie doesn't fully begin to realize her own femininity until she can prove useful to her mother in childbirth. As Francie discovers her desire for companionship, she begins to understand the injustices women are often forced to endure when pregnant out of wedlock.
Other issues the book addresses include:
- Man vs. his environment
- Coming of age/loss of innocence
- The American Dream