No no, a free water depth is correct if your boundary is fluvial (I mean Froude number less than 1). So the variation of the discharge at this boundary is not normal and this is a problem somewhere, to my opinion it can be explained only by strong variations or oscillations of depth at this level. Check if you have dry zones on this entrance (and if you declared TIDAL FLATS : YES if you have dry zones, this could be a hint), try a simpler velocity profile (1 for example), but well that cannot explain the problem, there is certainly something else.
JMH