If I had to guess at your problem is that you have your model layer defined as CONVERTIBLE (variable transmissivity/unconfine flow) rather than CONFINE. If you have a convertible layer with a head below the bottom of the cell it becomes "DRY" and is not included
in the simulation. This creates a conundrum if you have a constant head set to value below the bottom of the cell because a convertible layer marks it as DRY but the constant head says there is water there. CONFINE layers allow for the head to go below the
bottom of the cell.
The same goes for your initial head, if you give it a water level that is below the bottom of an active cell then it technically immediately becomes dry.
Some fixes is to either make the layer CONFINE, enable WETing, set the IBOUND=0 for those cells, or just make the starting head slightly above the bottom of the cell.
MODFLOW by default makes all IBOUND=0 cells no flow. So anywhere you have IBOUND=0 is analogous to solid rock/no flow.
Hope that helps out,
Scott
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