In an unstructured 2D mesh the quality can be checked by means of checking the aspect ratio of the individual triangles or even the edge growth ratio. This paper wants to show how the orientation of the triangles can also affect the model results. An estimation of the longitudinal and lateral numerical diffusion is given explaining why flow alignment can be beneficial in reducing the numerical diffusion. This is demonstrated for the advection of a tracer with the rotating cone example. The paper also shows an example of a 3D hydrodynamic model of the Scheldt estuary. A comparison is made between a good quality mesh and a flow aligned mesh for the same model domain. All variables are kept equal. The influence on tidal propagation is shown. The effect on the bottom friction coefficient is shown and the potential effect on a coupled sediment transport model is discussed. The flow aligned mesh reduces the amount of lateral numerical diffusion, it reduces the artificial loss of tidal energy along the estuary, and it improves the calibration result by getting more realistic bottom friction coefficients.