Heavy metal and metalloid contamination of topsoils from atmospheric deposition and release from landfills, agriculture, and industries is a widespread problem that is estimated to affect >50% of the EU's land surface. Influx of contaminants from soil to groundwater and their further downstream spread and impact on drinking water quality constitute a main exposure risk to humans. There is increasing concern that the present contaminant loading of groundwater and surface water systems may be altered, and potentially aggravated, by ongoing climate change, through large-scale impacts on recharge and groundwater levels. We investigated this issue by performing hydrogeological-geochemical model projections of changes in metal(loid) (As and Pb) mobilization in response to possible (climate-driven) future shifts in groundwater level and fluctuation amplitudes. We used observed initial conditions and boundary conditions for contaminated soils in the temperate climate zone. The results showed that relatively modest increases (0.2 m) in average levels of shallow groundwater systems, which may occur in Northern Europe within the coming two decades, can increase mass flows of metals through groundwater by a factor of 2–10. There is a similar risk of increased metal mobilization in regions subject to increased (seasonal or event-scale) amplitude of groundwater levels fluctuations. Neglecting groundwater level dynamics in predictive models can thus lead to considerable and systematic underestimation of metal mobilization and future changes. More generally, our results suggest that the key to quantifying impacts of climate change on metal mobilization is to understand how the contact between groundwater and the highly water-conducting and geochemically heterogeneous topsoil layers will change in the future.