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Groundwater recharge modelling with MIKE SHE

Quantify catchment-scale groundwater recharge for abstraction permitting and water resource planning

 

The textbook definition of recharge as rainfall infiltrating into soil applies only under highly simplified conditions. At the catchment scale, soil moisture dynamics, lateral overland flow and interactions between the vadose zone and groundwater system fundamentally control both the location and magnitude of recharge. These processes can be simulated in an integrated framework that generates spatially distributed recharge rates and is calibrated against both river discharge and groundwater head observations - the most comprehensive approach for assessing groundwater resources and supporting water resource planning under changing climate conditions.

 

 

 

 

The problem

Groundwater recharge cannot be directly measured at the catchment scale. Lysimeters provide only point-scale estimates for specific soil types, while classical approaches infer recharge as a residual of the water balance, propagating uncertainties from all other terms. These methods also rely on quasi-stationary assumptions that are increasingly invalid under changing land use and climate conditions.

 

Baseflow Index methods (1950s–70s) estimated recharge from river baseflow, but in catchments where aquifers extend beyond the river network, groundwater can leave the system without reaching streams, leading to systematic underestimation. GIS-based HRU approaches (1980s–90s) introduced distributed land use and precipitation, yet calibration against river discharge alone assumes overland flow exits the catchment immediately, neglecting re-infiltration at valley margins where focused recharge can be significant.

 

 

Why it matters

The consequence of every existing method is uncertainty. Abstraction permits set against overestimated recharge draw down aquifers faster than they recover, triggering regulatory challenge and water stress. Designing dewatering measures for building infrastructure or mining activities with underestimated recharge rates can cause project delays and financial issues. With agricultural soil treatment, shifting land use and changing precipitation patterns altering groundwater table dynamic behaviour across planning horizons of decades, stationary BFI and GIS estimates are no longer a defensible basis for valid resource decisions. Estimating recharge correctly requires a model that simultaneously simulates unsaturated flow, overland flow, and saturated groundwater, calibrated against groundwater heads, not only river discharge.

Physics-based model

Workflow

Step 1: Define the model domain

Export MODFLOW/FEFLOW cells as a polygon shapefile or delineate the domain in GIS using a DEM, hydrogeological maps and rivers.

Step 2: Gather and preprocess datasets

Collect a DEM, precipitation/PET timeseries, soil data, and groundwater table distribution as a minimum.

Step 3: Build and run the model

Convert Excel/GIS datasets to native MIKE formats via the MIKE Zero toolbox, then configure inputs through the MIKE SHE GUI.

Step 4: Evaluate the results

Validate recharge outputs using MIKE SHE's timeseries plots, raster inspection, or Water Balance tool before exporting.

Step 5: Import into MODFLOW or FEFLOW

Use the provided FloPy/MIKE IO Jupyter Notebooks to export a RCH file for MODFLOW, or use FEFLOW 7's native dfs2 import directly. See here

Video: How to build a model in MIKE SHE

All steps to build a simple groundwater recharge model are covered in the free on-demand webinar: ​How to build a model in MIKE SHE - Part I

Build high-res groundwater recharge inputs for MODFLOW and FEFLOW

Join our live webinar on 22 July led by MIKE SHE experts, followed by a 20-minute Q&A session.

Importing the recharge into MODFLOW and FEFLOW

Want to learn more?

Register for our recharge modelling webinar or contact us to learn how to apply recharge modelling in your projects.

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