Water exchanges between a karstic conduit and the surrounding aquifer are driven by hydraulic head gradient at the interface between these two domains. The case-study presented in this paper investigates the impact of the geometry and interface conditions around a conduit on the spatial distribution of these exchanges. Isotopic (δ18O and δD), discharge and water head measurements were conducted at the resurgences of a karst system with a strong allogenic recharge component (Val d’Orléans, France), to estimate the amounts of water exchanged and the mixings between a saturated karstic conduit and the surrounding aquifer. The spatio-temporal variability of the observed exchanges was explored using a 2D coupled continuum-conduit flow model under saturated conditions (Feflow®). The inputs from the water heads and stable water isotopes in the groundwater flow model suggest that the amounts of water flowing from the aquifer are significant if the conduit flow discharges are less than the conduit flow capacity. This condition creates a spatial distribution of exchanges from upstream where the aquifer feeds the conduit (recharge area) to downstream where the conduit reaches its maximum discharge capacity and can feed the aquifer (discharge area). In the intermediate transport zone no exchange between the two domains takes place that brings a new criterion to delineate the vulnerable zones to surface water. On average, 4% of the water comes from the local recharge, 80% is recent river water and 16% is old river water. During the November 2008 flood, both isotopic signatures and model suggest that exchanges fluctuate around this steady state, limited when the river water level increases and intensified when the river water level decreases. The existence of old water from the river suggests a transient storage at the aquifer/conduit interface that can be considered as an underground hyporheic zone.