Sustainable groundwater management implies a good knowledge of recharge processes, especially in areas with water deficit, like the semi-arid region of Banabuiú watershed (Ceará State, Northeast of Brazil). In this zone, phreatic aquifers consist of Precambrian crystalline fractured reservoirs characterised by a high spatial anisotropy, both in terms of hydrodynamics and water quality. This study implemented a multi-tracer approach (18O, 2H, 14C, 3H, CFC, SF6), combined with hydrodynamic data (i.e. groundwater levels) to identify the groundwater recharge origin and the recharge mechanisms, and to estimate the groundwater residence time. At the basin scale, hydrodynamic data and local observations indicated the high reactivity of aquifers to precipitation and suggested that infiltration processes occur mostly through preferential infiltration zones. Stable isotope data showed a major contribution of evaporated surface water in the recharge process from many artificial or natural ponds. Groundwater residence time determination highlighted the spatio-temporal heterogeneity of flow path organisation within aquifers, with variable contributions between fast vertical flow (present-day end-member; 15-85 %) and a slower horizontal flow (old end-member <1960), underlining the vulnerability of aquifers to present-day environmental stress or pollution.