Bert Thomas is husband to Joanna Thomas and father to their five children: Eliza, Horace, Edward, Harry, and Noah. Following her parents' deaths, he also becomes guardian to Anne Shirley, though his guardianship is characterized by neglect and failure to provide emotional or physical stability. Chronic laziness and severe alcoholism prevent him from maintaining steady employment; earnings from sporadic odd jobs are typically spent on cheap liquor rather than family necessities. This addiction fuels domestic abuse, including physical violence toward Joanna, even during her pregnancies, significantly contributing to the family's dysfunction and financial strain. His behavior forces Anne and the eldest daughter Eliza into premature roles as caretakers for the younger children.

Despite his overwhelmingly negative traits, rare moments of paternal concern occur, such as when he urgently secures medicine to save his infant son Noah from hypothermia. These instances, however, are overshadowed by his general unrepentant nature, including verbal abuse toward Joanna, who shoulders the household's economic burdens. His character deteriorates further as the narrative progresses, with worsening alcoholism rendering him unrecognizable from any earlier semblance of responsibility. His death in a train accident ultimately frees the family from his destructive presence, allowing Joanna and the children to rebuild their lives in greater peace and happiness. His legacy is marked by familial trauma and economic hardship, though the family's recovery and correspondence with Anne indicate a path toward healing made possible by his absence.