This paper presents the modelling results of several tracer-tests performed in the cave system of Han-sur-Lesse (South Belgium). In Han-sur-Lesse, solute flows along accessible underground river stretches and through flooded areas that are rather unknown in terms of geometry. This paper focus on the impact of those flooded areas on solute transport and their dimensioning. The program used (One-dimensional Transport with Inflow and Storage: OTIS) is based on the two-region non equilibrium model that supposes the existence of an immobile water zone along the main flow zone in which solute can be caught. The simulations aim to replicate experimental breakthrough curves (BTCs) by adapting the main transport and geometric parameters that govern solute transport in karst conduits. Furthermore, OTIS allows a discretization of the investigated system, which is particularly interesting in systems presenting heterogeneous geometries. Simulation results show that transient storage is a major process in flooded areas and that the crossing of these has a major effect on the BTCs shape. This influence is however rather complex and very dependent of the flooded areas geometry and transport parameters. Sensibility tests performed in this paper aim to validate the model and show the impact of the parametrization on the BTCs shape. Those tests demonstrate that transient storage is not necessarily transformed in retardation. Indeed, significant tailing effect is only observed in specific conditions (depending on the system geometry and/or the flow) that allow residence time in the storage area to be longer than restitution time. This study ends with a comparison of solute transport in river stretches and in flooded areas.