The diverse landscapes of the Intermountain Adaptation Partnership (IAP) region contain a broad range of aquatic habitats and biological communities. A number of aquatic species are regional endemics, several are threatened or endangered under the U.S. Endangered Species Act (ESA), and many have declined because of the introduction of nonnative aquatic species, habitat fragmentation, and human development. Environmental trends associated with human-caused climate change have been altering the habitats of these species for several decades (Barnett et al. 2008; Hamlet and Lettenmaier 2007; Luce and Holden 2009; Mote et al. 2005), and more significant changes are expected during the 21st century (chapters 3, 4). For animals that live in or near aquatic environments such as fishes, amphibians, crayfish, mussels, and aquatic macroinvertebrates, changes in habitat and hydrological regimes are expected to shift their abundance and distribution (Ficke et al. 2007; Hauer et al. 1997; Poff et al. 2002; Rieman and Isaak 2010; Schindler et al. 2008). This is primarily because many of these species are ectothermic; thus, thermal conditions dictate their metabolic rates and most aspects of their life stages—how fast they grow and mature, whether and when they migrate, when and how often they reproduce, and when they die (Magnuson et al. 1979). Buffering these changes are the topographic diversity and steep environmental gradients of many landscapes throughout the IAP region, which contribute to slow climate velocities (sensu Loarie et al. 2009) and often create climate refugia where populations of many species can persist under all but the most extreme climatic changes (Isaak et al. 2016a; Morelli et al. 2016).