The main aim of this study was to predict current and future flood susceptibility under three climate change scenarios of RCP2.6 (i.e., optimistic), RCP4.5 (i.e., business as usual), and RCP8.5 (i.e., pessimistic) employing four machine learning models, including Gradient Boosting Machine (GBM), Random Forest (RF), Multilayer Perceptron Neural Network (MLP-NN), and Naïve Bayes (NB). The study was conducted for two watersheds in Canada, namely Lower Nicola River, BC and Loup, QC. Three statistical metrics were used to validate the models: Receiver Operating Characteristic Curve, Figure of Merit, and F1-score. Findings indicated that the RF model had the highest accuracy in providing the flood susceptibility maps (FSMs). Moreover, the provided FSMs indicated that flooding is more likely to occur in the Lower Nicola River watershed than the Loup watershed. Following the RCP4.5 scenario, the area percentages of the flood susceptibility classes in the Loup watershed in 2050 and 2080 have changed by the following percentages from the year 2020 and 2050, respectively: Very Low = −1.68%, Low = −5.82%, Moderate = +6.19%, High = +0.71%, and Very High = +0.6% and Very Low = −1.61%, Low = +2.98%, Moderate = −3.49%, High = +1.29%, and Very High = +0.83%. Likewise, in the Lower Nicola River watershed, the changes between the years 2020 and 2050 and between the years 2050 and 2080 were: Very Low = −0.38%, Low = −0.81%, Moderate = −0.95%, High = +1.72%, and Very High = +0.42% and Very Low = −1.31%, Low = −1.35%, Moderate = −1.81%, High = +2.37%, and Very High = +2.1%, respectively. The impact of climate changes on future flood-prone places revealed that the regions designated as highly and very highly susceptible to flooding, grow in the forecasts for both watersheds. The main contribution of this study lies in the novel insights it provides concerning the flood susceptibility of watersheds in British Columbia and Quebec over time and under various climate change scenarios.