A significant increase in surface water salinization in low-lying deltas is expected globally due to saline groundwater exfiltration driven by rising sea levels and decreasing freshwater availability. Sustaining fresh water-dependent agriculture in such areas will entail an increased demand for fresh water flushing. Unfortunately, the flushing of surface water is not operationally optimised and results in excessive use of scarce freshwater. To meet the increased demand for flushing, while minimizing the need for diverted freshwater, new operational designs are required. This paper presents a novel network model based approach that uses De Saint Venant (SV) and Advection Dispersion (AD) equations to optimize multiple objectives on water level and salinity control using a Nonlinear Model Predictive Control (NMPC). The resulting NMPC problem is solved with a receding horizon implementation, where the nonlinear program (NLP) at each iteration is solved using state-of-the-art large scale interior point solver (IPOPT). We evaluate the performance of the proposed approach and compare it to the traditional fixed flushing for a representative Dutch polder. Firstly, the approach is shown to be capable of controlling the water level and salinity level in the polder. Secondly, the results highlight that the network of canals, which were originally made for drainage, could not be made sufficiently fresh with current intake capacity. A simple design approach was used to identify appropriate new capacities for two of the gates that allow optimal flushing to guarantee the required water level and salinity constraints.