Cities under high exploitation of groundwater resources face severe problems of land subsidence due to pumping. This complex problem was addressed from earlier versions of MODFLOW as MODFLOW 2000 and has two packages: MODFLOW SUB and for its simulation with different options for the conceptualization and numerical modeling of normal aquifers and low conductivity interbeds.
Scientific research and professional consulting on the field of land subsidence modeling is limited; this scarcity might be because the coupled complexity of the appliance of numerical groundwater modeling and consolidation theory.
There is an effort to provide a simple problem of land subsidence on a heterogeneous aquifer on a graphical user interface as Model Muse. while real cases might require extensive observed datasets with pumping records from earlier stages of groundwater exploitation. This tutorial is a simple but comprehensive example of land subsidence simulation with MODFLOW-SUB and Model Muse, the tutorial has the model conceptualization, aquifer definition, datasets setup, boundary conditions construction, simulation and output representation.
It is highly recommended to review the MODFLOW 2005 and MODFLOW-SUB documentation that you can fin on these links:
MODFLOW 2005: https://pubs.usgs.gov/tm/2005/tm6A16/PDF/TM6A16.pdf
You can download the input data from this link.