Arctic and Subarctic environments are among the most vulnerable regions to climate change. Increases in liquid precipitation and changes in snowmelt onset are cited as the main drivers of change in streamflow and water temperature patterns in some of the largest rivers of the Canadian Arctic. However, in spite of this evidence, there is still a lack of research on water temperature, particularly in the eastern Canadian Arctic. In this paper, we use the CEQUEAU hydrological‐water temperature model to derive consistent long‐term daily flow and stream temperature time series in Aux Mélèzes River, a non‐regulated basin (41 297 km2) in the eastern Canadian subarctic. The model was forced using reanalysis data from the fifth‐generation ECMWF atmospheric reanalyses (ERA5) from 1979 to 2020. We used water temperature derived from thermal infrared (TIR) images as reference data to calibrate CEQUEAU's water temperature model, with calibration performed using single‐site, multi‐site, and upscaling factors approaches. Our results indicate that the CEQUEAU model can simulate streamflow patterns in the river and shows excellent spatiotemporal performance with Kling‐Gupta Efficiency (KGE) metric >0.8. Using the best‐performing flow simulation as one of the inputs allowed us to produce synthetic daily water temperature time series throughout the basin, with the multi‐site calibration approach being the most accurate with root mean square errors (RMSE) <2.0°C. The validation of the water temperature simulations with a three‐year in situ data logger dataset yielded an RMSE = 1.38°C for the summer temperatures, highlighting the robustness of the calibrated parameters and the chosen calibration strategy. This research demonstrates the reliability of TIR imagery and ERA5 as sources of model calibration data in data‐sparse environments and underlines the CEQUEAU model as an assessment tool, opening the door to its use to assess climate change impact on the arctic regions of Canada.