Large rivers constitute small portions of drainage networks but provide important migratory habitats and fisheries for salmon and trout when and where temperatures are sufficiently cold. Management and conservation of cold‐water fishes in the current era of rapid climate change requires knowing how riverine thermal environments are evolving and the potential for detrimental biological impacts. Robust estimates of warming rates, however, are lacking due to limited long‐term temperature monitoring, so here we compile the best available multi‐decadal records and estimate trends at 391 sites in the 56,500 km river network of the northwestern U.S. Warming trends were prevalent during summer and early fall months in recent 20‐year and 40‐year periods (0.18-0.35 °C/decade during 1996-2015 and 0.14-0.27 °C/decade during 1976-2015), paralleled air temperature trends, and were mediated by discharge trends at regional and local levels. To illustrate the biological consequences of warming later this century, trend estimates were used to inform selection of river temperature scenarios and assess changes in thermal exposure of adult sockeye salmon migrating to four population areas as well as thermal habitat shifts for resident brown trout and rainbow trout populations throughout the region. Future warming of 1-3 ᵒC would increase sockeye salmon exposure by 5-16% (3-143 degree‐days) and reduce thermally suitable riverine trout habitats by 8-31% while causing their upstream shift. Effects of those changes on population persistence and fisheries are likely to be context dependent and strategic habitat restoration or adaptation strategies could ameliorate some biological impairments but effectiveness will be tempered by the size of rivers, high costs, and pervasiveness of thermal effects. Most salmon and trout rivers will continue to provide suitable habitats for the foreseeable future but it also appears inevitable that some river reaches will gradually become too warm to provide traditional habitats.