If you have ponded water on the surface of your model, you should set the depth to a negative value. The example below represents 30m of ponded water. Also, see the Groundwater Analysis section of the Settle3D Online Help for information on setting the depth parameter. Here is an excerpt from the Online Help:
To define a water table above the ground surface, enter the Depth as a negative number. In this case, it is assumed that the ground surface is submerged under a layer of ponded water, and the weight of the ponded water will be accounted for in the analysis. If embankment loads are defined, the buoyant unit weight will be used for the submerged portion of the embankment.