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Among different uses of freshwater, irrigation is the most impacting groundwater resource, leading to water table depletion and possible seawater intrusion. The unbalance between the availability of water resources and demand is currently exacerbated and could become worse in the near future in accordance with climate change observations and scenarios provided by Intergovernmental Panel on Climate Change (IPCC). In this context, Increasing Maximum Capacity of the surface reservoir (IMC) and Managed Aquifer Recharge (MAR) are adaptation measures that have the potential to enhance water supply systems resiliency. In this paper, a multiple-users and multiple-resources-Water Supply System (WSS) model is implemented to evaluate the effectiveness of these two adaptation strategies in a context of overexploited groundwater under the RCP 4.5 and the RCP 8.5 IPCC scenarios. The presented a case study that is located in the Puglia, a semi-arid region of South Italy characterized by a conspicuous water demand for irrigation. We observed that, although no significant long-term trend affects the proposed precipitation scenarios, the expected temperature increase highly impacts the WSS resources due to the associated increase of water demand for irrigation purposes. Under the RCP 4.5 the MAR scenario results are more effective than the IMC during long term wet periods (typically 5 years) and successfully compensates the impact on the groundwater resources. Differently, under RCP 8.5, due to more persistent dry periods, both adaptation scenarios fail and groundwater resource become exposed to massive sea water intrusion during the second half of the century. We conclude that the MAR scenario is a suitable adaptation strategy to face the expected future changes in climate, although mitigation actions to reduce green-house gases are strongly required.