Surface water salinization in deltaic areas due to saline groundwater exfiltration is an important issue. Saline surface water will not be appropriate for drinking water production, agricultural and industrial use, and therefore, freshwater diverted from rivers is used for flushing the canals and ditches in coastal areas. The effects of climate change, sea level increase and fresh water availability increases the stress on deltaic areas resulting in questioning current fresh water management strategies. In this paper, a Model Predictive Control (MPC) scheme is developed and tested for combined salinity and water level control of a polder ditch. The MPC scheme is coupled with Rapid Saline Groundwater Exfiltration Model (RSGEM) developed for fast calculation of exfiltration flux and concentration in a low-lying polder. For the test case presented in this paper, real data from Lissertocht catchment in Netherlands is used for RSGEM to see the performance of the MPC scheme for a real scenario. With open space for further research, results presented on this paper show that MPC of salinity in polders is capable of dealing with saline groundwater exfiltration modeled by RSGEM.Keywords: Modeling and identification of environmental systems, Real-time control of environmental systems, Hydroinformatics, Climate change impact and adaptation measures, Water quality and quantity management, Water prediction and control.