Hello robinson2012,
What is the bottom elevation of the point where you are looking at the free surface elevation time evolution in Figure tide01.PNG? If it is around 0.5 m, your result is normal, as the water depth cannot be lower that 0 m (or a little bit depending on which option you choose when you have tidal flats). If it is less than 0.5 m, do you have any tidal flats near this point in the estuary?
I suppose that inside the estuary, there may be tidal flats, may not there? If yes, in addition to default options (search for TIDAL FLATS in the dictionnary), you can use the option TREATMENT OF NEGATIVE DEPTHS = 2 (+ SUPG = 0), then you should not have negative depths on tidal flats, it is more physical.
Anyway, I have quickly looked at your steering file, and I have a few remarks to give you (that should not change the physics of your results). It is not improper, but can be improved a little bit.
In the validation directory, you can look at 123_tide test case which is a coastal study where tides are modelled. Used options are advised for such kind of studies. Moreover, you can read the topic
www.opentelemac.org/index.php?option=com...7&limitstart=10#6080 where some advice is given.
In your steering file, if you use the option TREATMENT OF LINEAR SYSTEM = 2 (wave equation), you should use SOLVER = 1 (conjugate gradient), it is more efficient (then, you can decrease SOLVER ACCURACY). If you had spurious oscillations for free surface or velocities, you could tune FREE SURFACE GRADIENT COMPATIBILITY (< 1.).
You seem to have written free surface elevation in the FORMATTED DATA FILE 1 (with the code 5 4 4 in the boundary conditions file I suppose), do you? If you also have velocities, you could use Thompson's conditions (OPTION FOR LIQUID BOUNDARIES = 2;1 if the 1st open boundary is marine) like other TELEMAC users (please see other posts), it is more physical. Moreover, if your domain is located inside the area of a local solution of tide from Oregon State University (TPXO-like), from version 6.2, you can use developments of TELEMAC. If you do not have points in your domain interpolated in tidal flats in the solution from OSU, it should work correctly.
Hope this helps,
Chi-Tuan