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"abstract": "Water temperature is a primary control on the health, diversity, abundance, and distribution of aquatic species, but thermal degradation resulting from anthropogenic influences on rivers is a challenge to threatened species worldwide. In the Willamette River Basin, northwestern Oregon, spring-run Chinook salmon (Oncorhynchus tshawytscha) and winter-run steelhead (O. mykiss) are formerly abundant cold-water-adapted species that are now protected under the Endangered Species Act. Among the challenges to the health of cold-water salmonids in the Willamette River Basin, disruptions in the seasonal patterns of stream temperature imposed by 13 large, multipurpose dams on tributaries to the Willamette River, as well as temperatures routinely in excess of regulatory limits in the Willamette River Basin, are contributing factors. To better understand controls on stream temperature, the sensitivity of stream temperature to flow augmentation as a management tool for suppressing high temperatures, and the implications for threatened salmonids, this study used a two-dimensional hydrodynamic and water-quality model (CE-QUAL-W2) to investigate spatial and temporal patterns of stream temperature in the Willamette River Basin. This study focused on the upper 160.4 river miles of the Willamette River from the confluence of the Middle Fork and Coast Fork Willamette Rivers (river mile 187.2) to Willamette Falls (river mile 26.8), three representative climate years (2011, a cool and wet year; 2015, an extremely hot and dry year; and 2016, a moderately hot and dry year), and a series of flow-augmentation scenarios. Model results show that the Willamette River upstream from Willamette Falls is divisible into four characteristic \u201cthermal reaches\u201d with similar thermal patterns, depending on tributary input, warming rate, and the timing of thermal response. In general, the Willamette River warms downstream during spring and summer, but patterns are complex, influenced by tributary inflows, and seasonally variable. Except in cool wet years (as illustrated by 2011), modeling suggests that adversely warm conditions for spring-run Chinook salmon are extensive from June or July through August. The thermal influence of flow augmentation from dam storage on four tributaries with U.S. Army Corps of Engineers dams varies spatially along the Willamette River, seasonally, and in magnitude, depending on a range of factors like distance from the Willamette River, the temperature of dam outflow, and the thermal template of tributary reaches controlling stream temperature adjustment to environmental heat fluxes. Modeling suggests that targeted flow management (via augmentation from dam storage) can reduce the extent and duration of thermally stressful conditions for Chinook salmon for short periods, but modeling suggests that flow augmentation is limited in its ability to fundamentally alter the \u201cthermal landscape\u201d (the entire range of temperature variation in a river system over space and time) of the Willamette River. While this research provides general insights into the thermal landscape of the Willamette River and its sensitivity to flow management, additional investigation into the thermal landscape of tributaries downstream from U.S. Army Corps of Engineers dams, as well as the thermal management of reservoirs, storage availability, and dam outflows, would be necessary to target specific management actions for supporting specified rearing or migration conditions for spring-run Chinook salmon and other cold-water-adapted species in the Willamette River Basin.",
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