Large-scale hydrologic–hydrodynamic models are powerful tools for integrated water resources evaluation at the basin scale, especially in the context of flood hazard assessment. However, recent model developments have paid little attention to simulate reservoirs’ hydrodynamics within river networks. This study presents an adaptation of the MGB model to simulate reservoirs as an internal boundary condition, enabling the explicit simulation of hydrodynamic processes along reservoirs and their interaction with upstream and downstream floodplains in large basins. A case study is carried out in the Itajai-Acu River Basin in Brazil, which has periodic flood-related disasters and three flood control dams. The model was calibrated for the 1950–2016 period forced with daily observed precipitation. The adjustment was satisfactory, with Nash–Sutcliffe metrics between 0.54 and 0.84 for the 11 gauges analyzed and with flood frequency curves also well represented. Simulation scenarios with and without floodplains and reservoirs were performed to evaluate the relative role of these factors on flood control basin-wide through evaluation of simulated discharges, water levels and flood extent. Itajai do Oeste tributary and Itajai-Acu mainstem present major floodplain attenuation, while in Itajai do Sul and Itajai do Norte tributaries the main flood control occurs due to reservoir attenuation. Downstream from the dams, results indicated that the reservoirs reach their maximum discharge reduction capacity for 5- to 10-year floods, decreasing it for larger floods. The developed model may be very useful for operational uses as flood forecasting and coordinated reservoir operation studies, as well as to enhance the comprehension of flood dynamics at basin scale.