Juvenile coho salmon thrive in intermittent streams of the Pacific Northwest yet are in danger of increased mortality. With more frequent climate extremes projected, the need to understand how intermittent stream hydrology and biogeochemistry impact juvenile salmonid habitat and behavior is imperative. Previous investigations indicated that dissolved oxygen limits the persistence of coho salmon in intermittent streams, leading to the hypothesis that groundwater inflow would ultimately control patterns of salmon recruitment and persistence. Here we tested that hypothesis in paired tributaries of Salmon Creek, Sonoma County, CA during California’s extreme drought of 2011-2017. Results suggested that coho salmon fry preferentially selected pools with a groundwater inflow signal and persisted in pools maintaining that signal through the dry season.