The low-lying coastal areas, and especially the delta areas are prone to saltwater intrusion due to sea level rise, which may lead to a loss of ecosystem services brought about by salinization of already limited freshwater reserves. Despite the acknowledged importance of climate change impacts and land use practices on water resources availability, there is still a lack of studies on the issue of climate change induced alteration of water quality. To understand the hydrogeochemical processes occurring within the shallow groundwater system of the Po River delta (Italy), the contribution of local water-sediment interaction and the anthropogenic influence on groundwater quality were quantified. High-resolution multi-level sampling was used to capture chemical gradients within the aquifer. Data were employed to calibrate a density-dependent multicomponent reactive transport model implemented with PHT3D code along a flow line. The reactive network accounted for redox driven organic matter oxidation and cation exchange. Finally, a series of numerical scenarios were run following the projection of IPCC 2014 on sea level rise and climate change. Results of the predictive model highlight an increase of arsenic and lead in the shallow portion of the aquifer, drained by the reclamation network. The increase of heavy metals export toward surface waters could be of serious concern, since the drainage network operates also for irrigation purposes. Thus, the surface water quality could be negatively affected by climate change.