Sam,
From the 2014 M21HD manual, section 6.12.3 on Inland Flooding:
[quote]In certain situations MIKE 21 may yield negative water depths. This can
occur for instance in areas with steep gradients in the bathymetry (or
topography) or by a relatively large time step in the model. To minimize
the potential for mass falsification you should generally use smaller flood
and dry levels for inland flooding. Appropriate values in inland flooding
could be Drying depth in the range 0.001 - 0.02 m and Flooding depth in
the range 0.002 - 0.04 m, where Flooding depth > Drying depth.
NOTE: The drying and flooding depth must be larger than 0.0001 m and
0.0002 m, respectively.
[/quote]
Hope this helps,
ab