<p>Abrupt flow changes from hydropower regulation, or ‘hydropeaking’, can cause sudden dewatering in rivers, but its interaction with climate change on aquatic organisms’ ontogenetic niche shifts is poorly understood. Hydropeaking is becoming increasingly common in regulated rivers, including those with populations of the threatened Atlantic salmon. This study examined how elevated temperatures, rapid flow fluctuations (simulating hydropeaking), and eyed-egg size affect Atlantic salmon survival, body mass, and emergence timing. Eyed-eggs in artificial redds were exposed to four treatments: normal temperature/stable flow, warm temperature/stable flow, normal temperature/rapid dewatering, and warm temperature/rapid dewatering. The normal temperature treatments followed the temperature regime of a nearby salmon river, while the warm treatments were elevated by three degrees. The individual emergence date from the artificial redds and fry body mass were recorded. Fish that did not survive to emerge were counted. Overall, rapid flow fluctuations decreased their probability of survival to emergence, reduced their body mass at emergence, and delayed their emergence timing. Elevated water temperatures also decreased their probability of survival, reduced their body mass, and caused them to emerge earlier than normal-temperature conspecifics. Eyed-egg size impacted survival and fry mass, with individuals from families with a large mean egg size slightly less likely to survive but more likely to have a large fry body mass than individuals from families with a low mean egg size. This study is the first to investigate the impacts of rapid flow fluctuations on emergent Atlantic salmon fry and has important implications for regulated rivers, particularly under climate change.</p>