Saline groundwater exfiltration to surface water increases the surface water salinization and degrades the surface water quality in low-lying deltaic areas. The use of surface water will be less appropriate for agricultural, industrial and drinking water production due to salinization, and therefore, freshwater diverted from river is used for flushing canals and ditches in these areas. Current water management strategies for flushing control in low lying polders have to be revised due to expecting negative effects of climate change, sea level increase and decreasing fresh water availability. Model predictive control (MPC) is a powerful control option which is increasingly used by operational water managers for managing water systems. The explicit consideration of constraints and multi-objective management are important features of MPC. In this study, a MPC scheme is developed and tested for combined salinity and water level control of a polder ditch. Saline groundwater exfiltration flux and concentration is modelled and used as known disturbances for the MPC scheme by using Rapid Saline Groundwater Exfiltration Model (RSGEM). The developed control scheme is tested on a test case using real data from a Dutch polder affected by high saline groundwater exfiltration to observe the performance of the controller for a real scenario. Simulation results show that MPC can increase the operational efficiency of flushing operations significantly.