A severe threat to natural resources and human livelihood is groundwater scarcity. Therefore, mapping groundwater potentiality (GWP) is necessary for future resource management. In this article, a framework for conducting ensemble modeling is introduced. This framework will be used to map GWP at the national level under the climate change scenario. Thirteen elements linked to topography, geology, hydrology, and land cover, as well as six climatic indicators based on historical time series data, were used to map the GWP. To provide extremely reliable groundwater potentiality mapping, three traditional standalone machine learning techniques such as logistic model tree (LMT), logistic regression (LR), and artificial neural network (ANN) have been merged with a stacking ensemble framework. Using the empirical and binormal receiver operating characteristic curves, the GWP mapping has been validated (ROC curve). According to research, Bangladesh's major rivers run along the high GWP zones in the country's southern and central regions. Additionally, the validation using the ROC curve demonstrates that the stacking model which had all three MLAs—performed better than other models (AUC: 0.971). The study may have a substantial impact on Bangladesh's national water planning and policy, which will be made using evidence. Additionally, the suggested method might be applied to map GWP on a broader scale in additional nations as well as at the continental level.