The Clockmaker’s Daughter is particularly concerned with the trauma caused by sudden loss and the impact that grief has on a person. All of the main characters are touched by grief in some manner, and they handle this loss in different ways. While the novel makes no judgment about how to approach bereavement, some characters handle their loss more successfully than others.

Birdie/Lily lost her mother early in her life and dealt with the absence of her father by believing that he was in America and would return for her. Just as she never blamed her father for leaving her, Birdie never blames Lucy for her death. While she initially feels despair upon learning she is a ghost and can no longer communicate with Edward, Birdie makes the best that she can of her circumstances by taking an interest in the visitors to Birchwood. Instead of being becoming a vengeful ghost, Birdie instead acts as a benevolent observer or even, where she can, a positive influence. She turns her loss to good by empathizing with the other broken, wounded souls who come to her house. Kate Morton hence subverts the tropes of ghost stories by exploring the influence of grief when a ghost is grieving their own life.