The Lake Ontario cisco Coregonus artedi population declined in the 20th century, and restoration of this species is a management objective. Management tools to restore cisco are limited because little is known about cisco spawning behavior and habitat use. We tagged 76 cisco from a remnant population in Chaumont Bay, Lake Ontario with acoustic transmitters and characterized seasonal habitat use from 2016 to 2021. We also used fine-scale acoustic telemetry, coregonine egg collections, and trap net catches to better understand cisco spawning behaviors related to spawn timing and site selection. Network analysis and Bayesian standard ellipse area indicated that cisco utilization of lake regions and bathythermal niche space varied by season. During spawning season, male cisco concentrated in Chaumont Bay over shallow (∼3 m) rocky shoals where cisco egg deposition was the greatest. Spawning site fidelity to Chaumont Bay was observed for all male cisco surviving to successive years (n = 23). Acoustic-tagged females did not survive consecutive spawning seasons, but trap net catches indicated females were less abundant and occupied spawning areas for less time than males. Post spawn, some individual male cisco (n = 5/23) had differential, yet consistent, annual migrations to separate regions of Lake Ontario, suggesting fidelity to feeding sites. Our results reveal seasonal habitats used by male cisco and, importantly, caution that environmental changes to a single spawning site could negatively affect the remnant Chaumont Bay cisco population. Specialized conservation efforts may be necessary when cisco spawning aggregations have diverse post-spawn migratory behaviors but a central spawning ground.