The aim of this study is to present a framework that provides new ways to characterize the spatio-temporal variability of lateral exchanges for water flow and solute transport in a karst conduit network during flood events, treating both the diffusive wave equation and the advection–diffusion equation with the same mathematical approach, assuming uniform lateral flow and solute transport. A solution to the inverse problem for the advection–diffusion equations is then applied to data from two successive gauging stations to simulate flows and solute exchange dynamics after recharge. The study site is the karst conduit network of the Fourbanne aquifer in the French Jura Mountains, which includes two reaches characterizing the network from sinkhole to cave stream to the spring. The model is applied, after separation of the base from the flood components, on discharge and total dissolved solids (TDSs) in order to assess lateral flows and solute concentrations and compare them to help identify water origin. The results showed various lateral contributions in space – between the two reaches located in the unsaturated zone (R1), and in the zone that is both unsaturated and saturated (R2) – as well as in time, according to hydrological conditions. Globally, the two reaches show a distinct response to flood routing, with important lateral inflows on R1 and large outflows on R2. By combining these results with solute exchanges and the analysis of flood routing parameters distribution, we showed that lateral inflows on R1 are the addition of diffuse infiltration (observed whatever the hydrological conditions) and localized infiltration in the secondary conduit network (tributaries) in the unsaturated zone, except in extreme dry periods. On R2, despite inflows on the base component, lateral outflows are observed during floods. This pattern was attributed to the concept of reversal flows of conduit–matrix exchanges, inducing a complex water mixing effect in the saturated zone. From our results we build the functional scheme of the karst system. It demonstrates the impact of the saturated zone on matrix–conduit exchanges in this shallow phreatic aquifer and highlights the important role of the unsaturated zone on storage and transfer functions of the system.