The Northern Basque Country (Southwestern France) is subject to a constant need of increasing water due to a rising population. The fissured aquifer of the Ursuya Mount is one of the main water supplies able to meet these needs. Unfortunately, there is a lack of knowledge on the residence time of groundwater and flow pattern in this strategic resource. Geochemical monitoring of groundwater was carried out from 2009 to 2011 in conjunction with CFC-SF6 measurement and with a detailed geological field characterization. It appears that groundwater flows and water geochemistry are conditioned by the development of a weathered layer overlying the fissured aquifer. When the weathered layer is absent, groundwater flows take place in unconfined conditions along fractures and fissures. The rapid circulation (mean residence time between 11 and 15 a) and the low solubility of the matrix generates low mineralization (mean about 61 μS cm−1). When a weathered layer is present, the flow depends on the degree of weathering, with groundwater circulating in the deep fissured zone in the case of a high degree of weathering. The apparent age is then between 10 and 42 a and the mineralization tends to increase concomitantly with the residence time, and particularly terrigenic element concentrations. In the case of a lesser degree of weathering, mixing between recent water from the shallow weathered layer and the oldest water (25 to >50 a) from the underlying fissured aquifer is observed. These results allow the definition of a conceptual model of flow characteristics in the study area which is also applicable to other weathered-fractured systems worldwide.