Due to climate change, low river discharges are expected more frequently. As a result, salt intrusion in the Rotterdam Waterway will be critical at least five times more frequently, negatively impacting freshwater availability. A possible new measure to reduce salt intrusion is providing additional mixing by internal wave generation, which reduces the estuarine circulation. The potential to reduce salt intrusion in the Rotterdam Waterway by internal wave generation is investigated. To determine this the irreversible mixing generated by internal waves is quantified and related to salt intrusion length. Numerical 2DV simulations of a decelerating flow over an undular bed were executed for an idealized section of the Rotterdam Waterway. The mixing was quantified by determining the background potential energy in a chosen control volume. This method can be applied if disturbances in the velocity or density profile do not reach the boundaries of the control volume. The mixing observed in the control volume is related to salt intrusion by the buoyancy frequency of the background state. The net salt flux imported by estuarine circulation was found to be proportional to the squared buoyancy frequency. Estuarine circulation is the main forcing mechanism of salt intrusion in the seaward part of the Rotterdam Waterway. For the small idealized section of the Rotterdam Waterway, internal waves generated over geometrical features are capable of reducing the salt intrusion caused by estuarine circulation by approximately 1.7% of the initial value, if bed waves are present over 27.5% of the control volume.