Exposure to the herbicide atrazine at environmentally relevant concentrations has been shown to negatively impact aquatic organisms, including crayfish. Because xenobiotics are concentrated in the crayfish hepatopancreas (digestive gland), we examined changes in morphology and DNA damage in hepatopancreatic tissue structure and cells following a 10-day exposure to atrazine (0, 10, 40, 80, 100 and 300 ppb). We found that there were marked morphological changes, post-exposure, for all atrazine concentrations tested. Hepatopancreatic tissue exhibited degenerated tubule epithelium with necrosis of microvilli, tubule lumen dilation and vacuolization of the epithelium. These changes increased in a dose-dependent manner. Likewise, we also performed a terminal deoxynucleotidyl transferase (TdT) mediated dUTP nick-end labeling (TUNEL) assay which showed the percentage of cells with DNA damage increased following atrazine exposure. Crayfish hepatopancreatic tissue displayed significant increases in TUNEL-positive cells following exposure to atrazine at 100 ppb and above. Overall, exposure to atrazine at environmentally relevant concentrations damages hepatopancreatic tissue, leading to an inability to detoxify atrazine and a potential to bioaccumulate atrazine long-term.