Identification and characterization of stream thermal refuges and associated habitat use by juvenile pacific salmon (Oncorhynchus SPP.) and steelhead (O. mykiss)

Cold-water patches can function as thermal refuges for juvenile Pacific salmon (Oncorhynchus spp.) and steelhead (O.mykiss) during periods of high summer stream temperatures. My study uses a three-phased approach to identify and classify thermal refuges in streams, characterize their environmental conditions during critical rearing periods, and monitor diel migration patterns of juvenile salmonids in response to environmental covariates. To identify thermal refuges, I used Remotely Piloted Aircraft System-based thermal infrared imaging. Repeat imaging of my study reach following a major channel-forming flood event in my second field season revealed that the composition of thermal refuges changed significantly, and that abundance of thermal refuges also increased. Specifically, the abundance of cold alcoves, a type of thermal refuge, increased eightfold following this flood. Cold alcoves are created by lateral shifts in stream channel alignments as part of the cut, fill, and avulsion processes associated with unconfined alluvial rivers. My results bring new evidence that flood processes of intact and unconfined floodplains provide an important role in maintenance and recruitment of thermal refuges in streams. In characterizing in situ temperature and groundwater conditions at thermal refuges, I installed temperature loggers and shallow streambed piezometers to collect time-series of temperature data and vertical hydraulic gradient – a measure of groundwater upwelling/downwelling conditions. Changes to these conditions were modelled in response to environmental covariates: mainstream stream temperature, air temperature, and stream discharge. Mainstem stream temperatures and mainstem thermal refuge temperatures were highly sensitive to changes in air temperature, and off-channel thermal refuge temperatures were least sensitive to changes in air temperature. The effects of stream discharge on thermal refuge temperature and vertical hydraulic gradient varied by site. Conspicuously, I observed that at some thermal refuges, short-term pulses of stream discharge from dam releases and atmospheric events drove inverse changes in groundwater upwelling. This evidence provides new considerations for regulated rivers that are counter to current understanding and common assumptions regarding hyporheic exchange and stream discharge. To characterize the diel horizontal migration patterns of juvenile salmonids at thermal refuges, I used Passive Integrated Transponder tags and arrays of antennae. Fish were captured, tagged, and released at identified thermal refuges over two summers. I logged and compiled fish-specific detections and determined migration type (i.e., immigration or emigration) based on the sequence of detections across multiple antennae. I fitted models for migration and occupancy at thermal refuges and found that, although fish differentially exploited cold-water patches during periods of high mainstem stream temperatures, stream and thermal refuge temperature were poor predictors of thermal refuge habitat use. Instead, diel horizontal migrations were highly correlated with photoperiod. Fish were found to enter mainstem habitats from thermal refuges at dusk and would make return migrations at dawn. Fish also exhibited thermal refuge site fidelity, and diel horizontal migrations continued into the fall after mainstem stream temperatures had cooled. My work provides new evidence regarding what triggers diel horizontal migrations in stream-dwelling juvenile salmonids, their occupancy at thermal refuge sites, and highlights the complexity of factors in their movement ecology.