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Anna Paulownapolder in the province of North Holland is characterized by high quality agriculture and valuable crops (tulip bulbs) which are salt sensitive. The polder is situated in the northern part of the Schermerboezem, near the Helsdeur at Den Helder. Salinization of the polder waters at the water inlet points is caused by opening the Helsdeur for navigation in the Schermerboezem causing water with high salt content to leak into the canal. The problem is of larger importance during summer when there are more ships and there is not enough rainfall to dilute the added salt. Therefore, the polder is flushed with IJsselmeer water during dry periods in order to replace the saline water with the fresh water. To better understand the origin of the salinity and Chloride concentration in the Anna Paulownapolder, SOBEK RR-CF-WQ was used to simulate the salinity transport in this area. SOBEK was applied both as a fine-scale (more detailed) model and as a coarse-scale (less detailed) model to see if the details of a SOBEK model can affect the simulation of the salinity transport in the area and represent more reliable outcomes. Both models were evaluated for wet and dry periods. Different variables such as water depth, water level and the water balance were checked to see whether the polder system was simulated properly. Next, a fraction analysis was performed to identify the origin of the salt in the area. Although, previous studies have shown that boil seepage is the most dominant cause of the salinity in low-land areas such as polders, boundary flow (i.e. Boezem inlet water) is the most dominant origin of the salt in the Anna Paulownapolder. Actually, seepage does not play an important role in the salinity of the Anna Paulownapolder. Two different scenarios were investigated by applying both models: 1) scenario 1, simulation of salt transport in the watercourses before the flushing event by IJsselmeer; 2) scenario 2, simulation of salt transport in the watercourses after the flushing event by IJsselmeer. In both scenarios, comparison of the simulation results with observations confirmed that the fine model resulted in more reliable outcomes than the coarse model.