Side weirs and overtopable levees are widely used to increase flood routing along a channel or river. The lateral loss of water reduces the sediment transport capacity leading to the formation of a local sediment deposit close to the overflow. Since the extent of the morphological bed changes is not known a priori, the design discharge is increased by this flow–sediment transport interaction in an uncontrolled way. Based on a systematic flume study, a semi-empirical model to predict the three-dimensional bed evolution of the aggraded channel reach in the vicinity of the overflow is developed. The shape of the deposit is modelled by an adapted Maxwell-type distribution function. The main input parameters of the model are expressed in terms of dimensionless parameters accounting for main channel and side overflow geometry as well as flow and sediment transport characteristics. The application of the empirical model in numerical flow calculations predicts 90% of the measured overflow.