One of Lily's internal struggles is whether or not to reveal the truth about her and Rosaleen. She cannot tell the truth to Augustus because she has not had good luck in the past trusting adults. Her father is abusive and her mother died when she was four. Feeling betrayed and abandoned by her parents, Lily finds a new home that she feels safe in - searching for her mother's origins and history. I think part of why Lily does not share who she is with Augustus is because part of her is afraid to learn about her mother's past and afraid to learn about what really happened the day her mother was shot and killed.
Another internal struggle of Lily is the racial issue present in the book. Lily is the only white girl in a house full of black women during the time of some serious racial tensions in America. Watching the news of race riots on television is very awkward for Lily, and she had a hard time not feeling guilty around the Boatwrights. Lily also finds herself developing a crush on Zach, Augustus's nephew. She knows they cannot be together because he is black and she is white. These societal expectations for how she should feel for the Boatwrights and Zach confuse how she truly feels for them. Zach at one point says "Lily, I like you better than any girl I’ve ever known, but you have to understand, there are people who would kill boys like me for even looking at girls like you" (135). She knows her close relationship with anyone of them could get them in trouble with the law, and therefore it makes it hard for her to act on her true feelings.