Water level amplification in harbour

My model is showing some water level amplification in a harbour area on the flood tide where water rushes in and out in cycles of about 40 mins (as shown in the attached plot).

This sloshing effect only seems to be present in the flooding tide, and not the ebb.

Unfortunately probes in the harbour are not showing these results. They are rather showing consistent rising and falling water level. Any ideas on why this is happened or ways I can resolve?

Samuel,

The program uses an Alternating Direction Implicit solver that can produce oscillations, although I wouldn't expect them to be so pronounced with reasonable settings (see pg. 13 of the M21HD_ScientificDoc). 

What time step and grid size have you used?  I would suggest cutting each in half (maybe more if they were unreasonably large to begin with) and observing the effect it has on your results, if you haven't already.  If the oscillations disappear or are significantly reduced then I would conclude it was just numerical error of the solution scheme.

Regards