Modelling the hydrology of North American Prairie watersheds is complicated because of the existence of numerous landscape depressions that vary in storage capacity. The Soil and Water Assessment Tool (SWAT) is a widely applied model for long-term hydrological simulations in watersheds dominated by agricultural land uses. However, several studies show that the SWAT model has had limited success in handling prairie watersheds. In past works using SWAT, landscape depression storage heterogeneity has largely been neglected or lumped. In this study, a probability distributed model of depression storage is introduced into the SWAT model to better handle landscape storage heterogeneity. The work utilizes a probability density function to describe the spatial heterogeneity of the landscape depression storages that was developed from topographic characteristics. The integrated SWAT–PDLD model is tested using datasets for two prairie depression dominated watersheds in Canada: the Moose Jaw River watershed, Saskatchewan; and the Assiniboine River watershed, Saskatchewan. Simulation results were compared to observed streamflow using graphical and multiple statistical criterions. Representation of landscape depressions within SWAT using a probability distribution (SWAT–PDLD) provides improved estimations of streamflow for large prairie watersheds in comparison to results using a lumped, single storage approach. Copyright © 2016 John Wiley & Sons, Ltd.