Nitrate contamination of groundwater remains a major concern despite all the measures and efforts undertaken over the last decades to protect water resources. We focused on a small catchment in Brittany (France) facing nitrate pollution with concentrations over the European drinking water standard of 50 mg.L−1. This is a common situation in catchments where - supposedly effective - measures were applied for reducing the transfer of N to groundwater. At the scale of this small (~100 ha) basement aquifer, nitrate concentrations are very heterogeneous in the groundwater, sampled up to 15–20 m below the soil surface in several observation wells (hereafter referred as piezometers) and up to 110 m deep in a borehole drilled through a faulted area near the Spring (outlet of the catchment). We used complementary and robust approaches for exploring and constraining the driving parameters of nitrate transfer and distribution in groundwater. Detailed geological work and a geophysical electrical resistivity tomography survey identified the lithologies, tectonic structures and weathering layers. This highlighted a complex geological structure with several compartments delimited by faults, as well as the highly variable thickness of the weathered layer. It also illustrated the heterogeneity of the hydrosystem, some compartments appearing to be disconnected from the general groundwater flow. This was confirmed by geochemical analyses and by the mean apparent groundwater residence time based on CFCs-SF6 and noble-gas analyses, locally revealing old and nitrate-free groundwater, and very old water with a recharge temperature below than the current average temperature in the area, reflecting water dating back to the last period of glaciation (−19 to −17 ky). Nitrate isotopes clearly showed denitrification processes in a few piezometers, which was generally supported by microbiology and molecular biology results. This highlighted the presence of functional genes involved in denitrification as well as a capacity of the groundwater microbial community to denitrify when in situ conditions are favourable. This type of combined approach - covering chemistry, isotopic methods, dissolved gases, microbiological activity, geophysics and hydrogeology - appears to be indispensable for implementing the most relevant programme of measures and for accurately assessing their effectiveness, notably by considering the timeframe between implementation of the measures and their impact on groundwater quality. © 2021 Elsevier B.V.