Abstract This paper presents research on the impact of a plan to change the salt-fresh water separation system at the Krammer locks in the Netherlands. This lock complex forms the connection for inland navigation between the Eastern Scheldt estuary and the hinterland. The new salt-fresh system will include bubble screens at both lockheads and an additional flushing discharge through the lock chambers and a neighbouring flushing sluice. The interaction between water management, salt management, ecology requirements and navigational requirements has been accounted for with the aid of WANDA-Locks and Delft 3D simulations. The effect of expected sea level rise on the performance of the new proposed new system is also modelled. The modelling efforts show that the new system should be able to keep the salt concentration of the fresh water lake Volkerak-Zoom within the required limits for the duration of the system’s technical lifespan. The modelling approach is able to tune the operation of the lock to the hydraulic conditions of each lockage and within the seasonal restrictions on the water management of the region, giving for each situation the required air discharge for the bubble screens and the flushing discharge. This operation has also been designed to remain safe for the vessels passing through the lock complex.