A study of siltation processes was undertaken for the harbour of Harlingen in the Netherlands, to investigate their relative importance for potential sedimentation. Three distinct harbour siltation processes were studied: tidal filling and emptying, horizontal eddy circulation in the harbour mouth and density driven vertical circulation. The Harlingen case, with its complex harbour geometry, seemed a promising candidate for a very early pilot application of D-Flow Flexible Mesh, a new hydrodynamic simulation code. Objective of this paper therefore was to investigate its performance, flexibility and efficiency by means of a qualitative comparison with an existing calibrated Delft3D curvilinear model. It was found that the flexible mesh allows for a more precise distribution of high resolution grid cells and capturing of complex geometries using a local triangular network. Moreover, the accuracy of the model was in line with existing Delft3D results. The tide and density driven current were found to be the main contributors to the siltation in Harlingen. Concluding, the applied research method combined with the Flexible Mesh approach look like a promising tool to help identify possible mitigating measures against harbour siltation problems.