Abstract. Flash floods pose significant hazards in urbanised zones and have important implications financially and for humans alike in both the present and future due to the likelihood that global climate change will exacerbate their consequences. It is thus of crucial importance to improve the models of these phenomena especially when they occur in heterogeneous and karst basins where they are difficult to describe physically. Toward this goal, this paper applies a recent methodology (Knowledge eXtraction (KnoX) methodology) dedicated to extracting knowledge from a neural network model to better determine the contributions and time responses of several well-identified geographic zones of an aquifer. To assess the interest of this methodology, a case study was conducted in southern France: the Lez hydrosystem whose river crosses the conurbation of Montpellier (400 000 inhabitants). Rainfall contributions and time transfers were estimated and analysed in four geologically delimited zones to estimate the sensitivity of flash floods to water coming from the surface or karst. The Causse de Viols-le-Fort is shown to be the main contributor to flash floods and the delay between surface and underground flooding is estimated to be 3 h. This study will thus help operational flood warning services to better characterise critical rainfall and develop measurements to design efficient flood forecasting models. This generic method can be applied to any basin with sufficient rainfall–run-off measurements.