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Within the Laurentian Great Lakes, many native fishes use wetlands for spawning; however, these areas are also used by non-native common carp (
Cyprinus carpio
) that may impart negative ecological impacts. There is interest in managing common carp using physical barriers to decrease passage to specific habitats (e.g., their spawning sites), but these barriers could also exclude native wetland spawners such as largemouth bass (
Micropterus salmoides
) and northern pike (
Esox lucius
). Our objective was to determine if differences in spawning movements could be exploited in shallow areas to operate seasonal barriers that are opened and closed to promote selective fragmentation. Using a long-term dataset from the Cootes Paradise Marsh Fishway (Hamilton, Ontario), we generated predictive models for spawning movements based on cumulative growing degree day (CGDD) for all three fishes. These models successfully predicted earlier arrival by all species in a warmer year and delayed spawning movements during a cold year, highlighting the role of temperature as a driver of interannual variation in spawning movements. We then compared the Fishway model predictions to spawning movements within nearby Toronto Harbour, which were derived from acoustic telemetry data. We found that the model outputs were correlated with movements of all three species, but performance was weakest for northern pike. Resource managers could use these predictive models to assist in the operation of seasonal barriers to decrease access of common carp to spawning sites, while maximizing passage to native fishes.