Hydrodynamic, hydrochemical, and isotopic investigations were carried out on 18 points, including boreholes, piezometers, and surface waters, from February 2011 to August 2012, to assess groundwater quality in the unconfined shallow alluvial aquifer of the Allier River (one of the main tributary of the Loire River). The study area, located near the city of Clermont-Ferrand (France), plays an important socio-economic role as the alluvial aquifer is the major source of drinking water for about 100,000 inhabitants. The objective of the project aims at understanding the functioning of alluvial aquifers that occupy a pre-eminent position in the hydrogeologic landscape both for their economic role - production of drinking water and agricultural development - and for their ecological role. Moreover, this study also targets at determining the factors and processes controlling shallow groundwater quality and origin. The water circulates from the south, with a natural alimentation from the hills in the non-pumped part of the alluvial aquifer. In the pumping zone, this general behaviour is altered by the pumping that makes the water from the Allier River enter the system in a large proportion. Four end-members have been identified for the recharge of the alluvial groundwater: rainfall, Allier River, surrounding hills' aquifer and the southern non-pumped part of the alluvial system. Results indicate that, despite the global Ca-HCO3 water type of the groundwater, spatial variations of physico-chemical parameters do exist in the study area. Ionic concentrations increase from the Allier River towards east due either to the increase in the residence time or a mixing with groundwater coming from the aquifer's borders. Stable isotopes of the water molecule show the same results: boreholes close to the river bank are recharged by the Allier River (depleted values), while boreholes far from the river exhibit isotopic contents close to the values of hills' spring or to the southern part of the alluvial aquifer, both recharged by local precipitation. One borehole (B65) does not follow this scheme of functioning and presents values attesting of a probable sealing of the Allier River banks. Based on these results, the contribution of each end-member has been calculated and the functioning of the alluvial system determined.