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Juvenile coho salmon thrive in intermittent streams of the Pacific Northwest yet are in danger of increased mortality from drought and rising temperatures. With warmer temperatures and 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. We used the fluorescent fingerprint of dissolved organic carbon, together with a parallel factor analysis, to estimate groundwater influence in individual stream pools, corroborating those estimates with stable isotope and radon analyses. Repeat snorkel surveys provided fish counts in those pools at the beginning and end of the period of surface-water disconnection. 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. This groundwater inflow signal was distinct from hyporheic influence, which exhibited little correlation with fish distribution. Groundwater within pools was young, and spot measurements suggested that it was relatively oxygenated. Proportional groundwater contributions to pools increased as drought deepened. Results suggest that maintaining relatively high groundwater levels in coastal aquifers may be imperative to the persistence of vulnerable salmonid populations in a changing climate.

Plain Language Summary In northern California and much of the Pacific Northwest, coho salmon thrive in intermittent streams that lack contiguous surface-water flow for part of the year. The young fish grow for 1year in these streams and may be particularly vulnerable to climate warming and extreme drought conditions. However, little is understood about the factors that promote young salmonid survival or demise during dry conditions. We evaluated the role of groundwater on fish persistence through a combination of fish snorkel surveys, dissolved oxygen measurements, and water sample collection and analysis. We found that all of the pools to which fish moved at the start of the summer dry period had groundwater inflow and that the oxygen content of that groundwater was moderately high. Fish persisted only in those pools that maintained groundwater inflow through the summer dry period. Groundwater inflow promotes circulation of water and may deliver oxygen to pools, both of which may enhance the chances of fish survival. Maintaining high groundwater levels during dry periods may thus be necessary for the long-term persistence of salmon in intermittent streams.