Side weirs are free overflow regulation and diversion structures commonly encountered in flood protection engineering. The lateral loss of water reduces the bed-load transport capacity in the main channel, leading to local sediment deposition near the side overflow. As a consequence, the design overflow is increased in an uncontrolled way. Since this flow–sediment interaction in such a channel has not been studied so far, systematic flume experiments have been performed. Based on these experiments, a two-dimensional empirical model to describe the longitudinal evolution of the aggraded channel reach near the weir has been developed. In addition, a simple and straightforward approach for direct estimation of the side overflow in presence of bed-load transport has been established. To be generally applicable in engineering practice, all input variables are expressed in terms of dimensionless parameters. Finally, the application of the models is demonstrated in a case study on the Rhone River in Switzerland.