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Groundwater quantity and quality degradation by agricultural practices is recorded as one of the most critical issues worldwide. This is explained by the fact that groundwater is an important component of the hydrological cycle, since it is a source of natural enrichment for rivers, lakes, and wetlands and constitutes the main source of potable water. The need of aquifers simulation, taking into account water resources components at watershed level, is imperative for the choice of appropriate restoration management practices. An integrated water resources modeling approach, using hydrological modeling tools, is presented for assessing the nitrate fate and transport on an over-exploited aquifer with intensive and extensive agricultural activity under various operational strategies and future climate change scenarios. The results indicate that climate change affects nitrates concentration in groundwater, which is likely to be increased due to the depletion of the groundwater table and the decrease of groundwater enrichment in the future water balance. Application of operational agricultural management practices with the construction and use of water storage infrastructure tend to compensate the groundwater resources degradation due to climate change impacts.