Hello Charlotta,
If I understand well the axis in your pictures, the bay would be about 25 km long, and I see 43 oscillations in 3 days, which is a period of about 6000 s, it cannot have numerical explanations. A long wave traveling through and back in the bay would do 50 km, and to do this in 6000 s we need a celerity of about 8.3, if this celerity is sqrt(gh) we get an average depth of 7 m, which is not too unrealistic, so it could be that you trigger a resonance in your bay with the boundary conditions.
A solution would be to try Thompson's boundary conditions, another would be to try relaxation, it consists in choosing a parameter alfa and giving as boundary condition for the free surface :
prescribed free surface = free surface at the previous time step
+ alfa(data - free surface at the previous time step)
with alfa less than 1 so that there is no sudden jump. This can be done also with Thompson by changing the hardcoded parameter that is commented in subroutine thomps.f (TETA at line 269). Depending on your time step a small parameter is certainly necessary to delay the free surface by a sufficient fraction of 6000 s so as to break the resonance.
Another interesting thing to know is the sampling period of the data, to know if the oscillations could have been filtered (such seiches do exist sometimes, in lake Léman for example). However such a resonance triggered by boundary conditions has already been reported once.
With best regards,
Jean-Michel Hervouet