Water temperature is a critical ecological indicator; however, few studies have statistically modeled century-scale trends in riverine or estuarine water temperature, or their cause. Here, we recover, digitize, and analyze archival temperature measurements from the 1850s onward to investigate how and why water temperatures in the lower Columbia River are changing. To infill data gaps and explore changes, we develop regression models of daily historical Columbia River water temperature using time-lagged river flow and air temperature as the independent variables. Models were developed for 3 time periods (mid-19 th , mid-20 th , and early 21 st century), using archival and modern measurements (1854–1876; 1938–present). Daily and monthly-averaged root-mean-square errors overall are 0.89°C and 0.77°C, respectively for the 1938–2018 period. Results suggest that annual averaged water temperature increased by 2.2 ±0.2°C since the 1850s, a rate of 1.3±0.1°C/century. Increased water temperatures are seasonally dependent. An increase of approximately 2.0 ±0.2°C/century occurs in the July–Dec time-frame, while springtime trends are statistically insignificant. Rising temperatures change the probability of exceeding ecologically important thresholds; since the 1850s, the number of days with water temperatures over 20°C increased from ~5 to 60 per year, while the number below 2°C decreased from ~10 to 0 days/per year. Overall, the modern system is warmer, but exhibits less temperature variability. The reservoir system reduces sensitivity to short-term atmospheric forcing. Statistical experiments within our modeling framework suggest that increased water temperature is driven by warming air temperatures (~29%), altered river flow (~14%), and water resources management (~57%).