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Climate change will affect the dynamics of the hydrogeological systems and their water resources quality; in particular nitrate, which is herein taken as a paradigmatic pollutant to illustrate the effects of climate change on groundwater quality. Based on climatic predictions of temperature and precipitation for the horizon of 2021 and 2050, as well as on land use distribution, water balances are recalculated for the hydrological basins of distinct aquifer systems in a western Mediterranean region as Catalonia (NE Spain) in order to determine the reduction of available water resources. Besides the fact that climate change will represent a decrease of water availability, we qualitatively discuss the modifications that will result from the future climatic scenarios and their impact on nitrate pollution according to the geological setting of the selected aquifers. Climate effects in groundwater quality are described according to hydrological, environmental, socio-economic, and political concerns. Water reduction stands as a major issue that will control stream-aquifer interactions and subsurface recharge, leading to a general modification of nitrate in groundwater as dilution varies. A nitrate mass balance model provides a gross estimation of potential nitrate evolution in these aquifers, and it points out that the control of the fertilizer load will be crucial to achieve adequate nitrate content in groundwater. Reclaimed wastewater stands as local reliable resource, yet its amount will only satisfy a fraction of the loss of available resources due to climate change. Finally, an integrated management perspective is necessary to avoid unplanned actions from private initiatives that will jeopardize the achievement of sustainable water resources exploitation under distinct hydrological scenarios.