Heat stress threatens the survival of Pacific salmonids at the southern extent of their range in Northern California and Southern Oregon. The high ecological, cultural, and economic value of Pacific Salmonids in this area has motivated a broad range of policy and management efforts aimed at supporting the persistence of these fish. These efforts will require user-friendly and scientifically informed decision-support tools. These tools must include mechanisms to identify and protect the sites that are most likely to support Pacific Salmonid persistence in warming surface water environments: sites known as thermal refugia.This dissertation focuses on a subset of cold water thermal refugia, those formed by cold water confluences with warm main river stems. It uses two such confluences in the South Fork Eel River in Northern California as case study locations, and the juvenile steelhead trout, Oncorhynchus mykiss, as a case study species. O. mykiss juveniles rear over the warm summer within the South Fork Eel River, and are exposed to heat stress in the warm main stem, which they are observed to escape from by holding in cold water confluence refugia. The dissertation synthesises approaches from fluid mechanics, hydrology, and ecology to refine the identification and definition of thermal refugia for O. mykiss, partly by exploring contradictions between the existing definitions and partly by linking fluid mechanics with fish bioenergetics to understand how fishes might use these refugia O.mykiss. Finally, the dissertation presents a mechanistic modeling framework for predicting the volume of available thermal refuge habitat at confluences. The framework is robust to non-stationary conditions and flexible enough to address the diverse physiological needs within a population of juvenile O.mykiss. By using parsimonious predictive approaches, the research generates tools to predict the extent of cold zones, and define their importance as thermal refugia for salmonids, over the large scales and multiple environments contained within river basin salmonid habitat.