AbstractWater competition in overallocated rivers is often extreme, and climate change exacerbates the challenge of balancing ecosystem and societal water needs. During a severe California drought in 2013–2014, storage in a strategic reservoir dropped to critically low levels, necessitating reduced downstream discharge during Chinook salmon, Oncorhynchus tshawytscha (Walbaum), incubation and rearing. In response, stakeholders developed an adaptive management process to balance competing water needs, including reservoir storage and salmon survival. This approach incorporated decision tree models, integrating salmon life stage transitions to define potential impacts. Life stage‐specific thresholds were identified and monitored to determine management triggers and actions. Flow reduction stranded up to 12% of incubating embryos and thus was used to trigger a flow pulse. Frequency of stranded fry in redds was reduced post‐pulse. Water quality did not change but remained within the species’ tolerance. High densities, poor body condition and aggressive behaviour of stranded fry triggered a second pulse three weeks later. This pulse reduced stranding and initiated downstream migration. Prescribed flow pulses supported outmigration of a keystone species while minimising water use during a critical period. This study evaluated ecological responses to management actions intended to ameliorate stressful low flow conditions and provided a decision‐making framework that can be used when resource use conflicts arise again.