Hi G.,
Modflow simulates stream-aquifer interaction by using River package in which three cases are there:
1. Stream stage is above the river bed elevation;
2. Stream stage is equal to river bed elevation;
3. and Stream stage is below the river bed elevation.
for simulating flow, MODFLOW uses standard formula where based on the relative elevation of the river stage and gw level, stream is characterized to be either gaining or losing. If the stream stage is below the river bed , as in ur case, MODFLOW uses river bed elevation instead of stream stage, in other words, once the stage level lower than the river bed, flow remains constant and will vary according to the level of aquifer.
Hope this
helps...
Regards
Vivek
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