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The study shows a significant net precipitation and surficial runoff decrease in the Province of Pesaro-Urbino during the 1950-2010 period, especially affecting mountain areas and the water-surplus winter season. Runoff variation is also related to a significant land use change, due to a progressive natural reafforestation process that has taken place in the mountain area. Candigliano river’s base-flow, fed by carbonate aquifers’ groundwater discharge, was found more stable over time, due to an aquifers’ capacity largely exceeding that of existing surface reservoirs. The latter have been affected by a significant silting process, which is still active, as suggested by specific erosion rates of watersheds, particularly in the Foglia basin. Important implications both on sediment mobility, surface water-supply reliability, minimum flow constraints and effectiveness of volume-recovery projects of reservoirs were preliminarly evaluated. In the perspective of a necessary adaptation process to the climate change, the study suggests a gradual transition from the present prevailing use of surface water, to an integrated management of the carbonate aquifers’ dynamic resources, on a seasonal base, as a sustainable strategy for the next future.