Groundwater pollution risk modelling is an important asset to improve groundwater management and protection. In this study, we assess the temporal dynamics of groundwater pollution risk at the continental scale, using the DRASTIC model. The approach was developed using continental-scale data on soil properties, topography, land use, geology, hydrogeology, and climate with a resolution of 15 × 15 km². We compared continental-scale groundwater pollution risk for the years 1990, 2000, and 2010. The results showed significant inter-annual variations of the spatial distribution of pollution risk. Changes were mainly concentrated in the area of the Nile Delta, around the Lake Victoria, in North Africa, and in coastal West Africa (predominately in Nigeria). We found that the increase in pollution risk was mainly related to the increase in the population density in these regions. The proposed methodology for modelling the temporal dynamics of groundwater pollution risk could support the monitoring of the Sustainable Development Goal 6, which focus in particular on the preservation of the freshwater resources against future threats.