This study developed the brook stickleback as a novel bioindicator species for assessing exposure to endocrine disrupting compounds in freshwater environments in Canada. Sex-specific genes were differentially expressed between male and female brook stickleback. Exposure to model androgens and estrogens induced the expected responses, with androgens inducing spiggin expression in females and estrogens inducing vitellogenin expression in males and increasing liver size. Transcript levels proved to be more sensitive biomarkers of hormone exposure than somatic indices. The brook stickleback showed potential for use in both laboratory and field studies of endocrine disrupting compound exposure.