The processes that occur in wetlands and natural lakes are often overlooked and not fully incorporated in the conceptual development of many hydrological models of basin runoff. These processes can exert a considerable influence on downstream flow regimes and are critical in understanding the general patterns of runoff generation at the basin scale. This is certainly the case for many river basins of southern Africa which contain large wetlands and natural lakes and for which downstream flow regimes are altered through attenuation, storage and slow release processes that occur within the water bodies. Initial hydrological modelling studies conducted in some of these areas identified the need to explicitly account for wetland storage processes in the conceptual development of models. This study presents an attempt to incorporate wetland processes into an existing hydrological model, with the aim of reducing model structural uncertainties and improving model simulations where the impacts of wetlands or natural lakes on stream flow are evident. The approach is based on relatively flexible functions that account for the input–storage–output relationships between the river channel and the wetland. The simulation results suggest that incorporating lake and wetland storage processes into modelling can provide improved representation (the right results for the right reason) of the hydrological behaviour of some large river basins, as well as reducing some of the uncertainties in the quantification of the original model parameters used for generating the basin runoff. Copyright © 2013 John Wiley & Sons, Ltd.