To understand the temporal and spatial variability of thermal refuges, this study focused on modeling potential thermal refuge area (PTRA) at a sub‐daily time‐step in two tributary confluences of the Sainte‐Marguerite River (Canada) during the summers of 2020 and 2021. Aquatic ectotherm species, such as Atlantic salmon (Salmo salar), seek these refuges to avoid heat stress during high summer river temperatures. To investigate the temporal variability of these PTRA, we employed inverse weighted distance interpolation to delineate the hourly area available at both confluences. We then analyzed the impact of the atypical low flow conditions of summer 2021 on the diel cycle of PTRA extremes using the coefficient of variation and the generalized additive model (GAM). Finally, we used four supervised machine‐learning regression models and three to five hydrometeorological predictors to estimate hourly PTRA availability: multivariate adaptive splines regression (MARS), GAM, support vector machine regression (SVM), and random forest regression (RF). The results showed that tree‐based and kernel‐based regression models, RF and SVM, outperformed GAM and MARS. RF had the highest accuracy at both sites, with a relative root mean square error and Nash–Sutcliffe efficiency coefficient (Nash) of 13% and 93%, respectively. Our study discovered that under warm conditions in August 2021, small perennial tributary inflows in combination with low mainstem discharge could create high and constant PTRA at confluences, potentially providing vital thermal refuges for cold‐water taxa. These refuges may be especially important at the local level, within a specific stretch or section of the river. Given the decreasing availability of thermal refuges for salmonids, it is crucial to monitor stream temperatures at small spatial and temporal scales using data‐driven techniques in order to understand stream temperature heterogeneity at tributary confluences.