Understanding the spatio-temporal variability of climate-induced river water temperature change is critical for identifying hotspots and assessing the impacts on ecological and socioeconomic systems. Here, we employ the air2stream model reconstructed river temperature records for 106 stations in Canada (Nash Sutcliffe coefficient goodness-of-fit: minimum = 0.79; median = 0.93; maximum = 0.97) to analyze summer temperature changes over the years 1980–2018. Results reveal widespread river temperature increases from June to September, with significantly increasing trends for about 40%–60% of stations. Additionally, we find significantly rising 7-day maximum temperature and increasing occurrences over the critical 18 and 20 °C thresholds for about 30%–65% of stations. Furthermore, by employing the Ward’s agglomerative hierarchical clustering machine learning (ML) method, we identify eight regions of spatially coherent variability and change. We find that the south-east, coast and northern prairies are the regions of high vulnerability because of the likely impacts of rising summer water temperatures on cold-water aquatic species. Additionally, by using the random forests ML method, we demonstrate that mean air temperature and its trends are the primary drivers of mean water temperature and trends, respectively. Thus, with the projected enhanced air temperature increase across Canada, an amplified future summer river warming can be expected, which could have severe consequences, particularly in already thermally-stressed river systems.