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Many species depend on water availability in low-order, headwater streams, which constitute the majority of streams in the Great Basin. Though these streams are important for a variety of reasons, we know very little about their current status (i.e., whether they are perennial or not) and potential responses to drought or other climate-related changes. To address these fundamental questions, we have deployed a series of instrument networks to track year-round patterns of temperature and flow permanence in focal watersheds in the northwest Great Basin, including southeast Oregon, northeast California, and northern Nevada. We have developed robust methods for determining both temperature and stream drying from instrumental records of temperature alone collected in stream channels. �Results from an intensively monitored watershed in southeast Oregon revealed spatially and temporally variable responses to recent wildfire (2012) and drought (2015). Overall, the system exhibited a high degree of climate sensitivity, with implications for vulnerability of threatened Lahontan cutthroat trout. �These findings have prompted a broader, collaborative effort to evaluate climate sensitivity of a much larger sample of streams managed for recovery of Lahontan cutthroat trout across the Great Basin. �Though trout are the focal species, results of this work will have important implications for�water-dependent wildlife, livestock grazing uses, and a variety of other values associated with water quality and availability in this arid landscape.