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Environmental monitoring was carried out in order to investigate the role of topsoil, rock matrix and fractures in controlling the water flow in unsaturated zone of calcareous rocks and in determining the timing and the magnitude of groundwater recharge. A comprehensive dataset of climate data, soil moisture and rock pressure heads was used to evaluate a physically based 1D dual permeability model, in order to simulate the water flow in the vertical profile to the groundwater table. The parameters of water retention and unsaturated hydraulic conductivity curves in soil and rock matrix were estimated using two evaporation experiments in the laboratory and the tension infiltrometer in the field. The other sensitive parameters of the model were calibrated using an optimization procedure based on combinations of randomly sampled parameters. Once the model had been calibrated, it was used to obtain insights into the hydrological processes through the unsaturated profile, down to the water table. The soil acts as a attenuation layer, determining the timing and the magnitude of drainage fluxes towards the unsaturated rock zone. The low permeability petrocalcic horizon below the soil, which frequently occurs in semi-arid regions, plays a key role in controlling the water exchanges between the soil and the rock. Most water flow in the top of the rock profile occurs through the fractures. This fracture flow becomes less along the profile, as a part of it gradually infiltrates into the unsaturated rock matrix. Fracture water infiltrates entirely into the matrix only when the unsaturated rock zone is very thick, so that in sites with a shallow water table fracture flow may be the dominant groundwater recharge mechanism. The flow through the matrix is continuous over time and at the water table it becomes constant and independent of large seasonal and annual variations in rainfall. The flow through the unsaturated matrix is the dominant groundwater recharge mechanism. In dry summers and in drought years the continuous matrix water flow sustains the recharge, thus maintaining high groundwater levels when more water is extracted. This is important in regions where groundwater from unconfined calcareous aquifers are important water resources. The recharge through the fractures is sensitive to the annual rainfall pattern and also contributes to the groundwater in years when the rainfall is greater. (c) 2010 Elsevier B.V. All rights reserved.