For a better understanding of the spatial variability of the hydrological response of catchments to flood events, the hydrological indicators obtained from annual water balances can be regionalized. However, many natural catchments are non-conservative, essentially due to interbasin groundwater flow (IGF) that hinders the application of water balances with traditional terms only, such as precipitation, streamflow and evapotranspiration. We thus carried out annual water balances including IGF on both conservative and non-conservative catchments of medium size (100-500 km(2)), subject to karst processes. To this end, we adapted the L'vovich annual water balance to account for IGF, including hydrograph separation and coupled it to a geomorphological analysis. Water balances were done at the elementary catchment scale, here either a headwater catchment, or an intermediate catchment delimited by two gauging stations. We applied this approach to 120 elementary catchments for which daily rainfall and runoff data were available. These catchments belong to 12 French drainage basins, located in partially or totally karstified regions (Cevennes, Jura, Normandy) subject to variable IGF depending on the extent of karst units. First, our results show that IGF can represent a significant part of the annual water balance, and that accounting for this component substantially improves the understanding of catchment processes. Second, several study sites showed correlations between hydrological and geomorphological parameters, providing interesting perspectives in terms of regionalization, in particular regarding ungauged basins. Our results provide a better understanding of the gains and losses affecting stormflow and baseflow components in catchments prone to important IGF..