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The Gulf of Maine Distinct Population Segment of Atlantic Salmon Salmo salar is listed under the U.S. Endangered Species Act, with dams cited as a key threat to the species. Safe, timely, and efficient passage of emigrating smolts is critical for advancing recovery goals. However, climate change and the earlier (and more variable) onset of smolt migration have challenged the effectiveness of measures designed to protect smolts. Therefore, we used data from four long‐term smolt trapping sites in Maine to characterize run duration, identify a standardized smolt run, and develop a predictive model for the initiation of smolt emigration for natural‐ and hatchery‐origin smolts. We combined these data into a basinwide deterministic model that projects the movement of smolts from their point of origin to estuary entry, which we used to (1) evaluate duration and temperature triggers for supplemental spill periods used at hydroelectric dams to protect smolts and (2) investigate how knowledge of smolt emigration dynamics can guide protective measures in rivers where management actions are being developed. Timing of run initiation varied by over 14 d; however, mean air temperature for the first quarter of the year explained over 60% of the variance in the onset of emigration. Initiation temperature was linked with higher‐elevation rearing areas where smolts originated and not with downstream dams where temperature was monitored. The shape of the smolt wave varied considerably; thus, our standardized smolt wave captured average dynamics but not the specific shape. Overall, 14‐d spill windows are too short. To account for the variable timing and shape of the run, a 54–72‐d protection window would be necessary to protect the earliest and latest emigrants in the absence of physical structures (e.g., turbine screens) and preserve the adaptive variation required for populations to respond to climate‐driven changes in temperature and hydrology. [ABSTRACT FROM AUTHOR]