Preprocessing of the Groundwater Level Map¶

A groundwater level map is required in several different MIKE SHE modelling workflows. Depending on the modelling approach, it can serve either as a fixed boundary condition, a calibration dataset, or an initial condition for transient simulations.

For recharge-only applications, where the fully coupled three-dimensional Saturated Zone module is not activated, the groundwater level map is used to define the fixed lower boundary condition of the Unsaturated Zone model. This workflow is commonly applied for groundwater recharge modelling, soil water balance studies, or overland flow simulations where groundwater flow itself is not simulated.

The same workflow is also recommended when developing a fully integrated MIKE SHE model with an active three-dimensional groundwater model. In this case, the groundwater level map serves two additional purposes.

First, it provides an independent reference dataset for evaluating the steady-state groundwater calibration. Comparing simulated groundwater heads with an observed groundwater level map allows the modeller to assess whether the simulated regional groundwater gradients and groundwater divides are physically plausible before proceeding to transient simulations.

Second, if no steady-state simulation is performed before the transient model is started, the groundwater level map can be used directly as the initial groundwater head distribution of the Saturated Zone model. Starting the simulation from physically meaningful groundwater levels generally reduces the numerical adjustment period and improves the stability of the transient simulation.

In many regions, officially published groundwater contour maps are available from national or regional hydrogeological authorities and provide an excellent starting point for deriving a groundwater level map. However, these maps are often generalized and may not adequately represent local groundwater conditions. Therefore, whenever groundwater monitoring data are available, it is recommended to combine both datasets into a single consistent groundwater level map.

The following workflow demonstrates how to derive such a groundwater level map within QGIS by combining regional groundwater contour maps with local groundwater observations.

Interpolation of Groundwater Contours¶

Load the groundwater contour lines into the QGIS project.
Verify that the contour lines contain an attribute representing the groundwater elevation values.
Open the Processing Toolbox and select an interpolation method, for example:
- TIN Interpolation
- IDW Interpolation
- Configure the interpolation settings:
- Input layer = Groundwater contour lines
- Interpolation attribute = Groundwater elevation
- Output extent = Data Collection Mask
- Horizontal resolution = 50 m
- Vertical resolution = 50 m
- Coordinate reference system = Project CRS
- Execute the interpolation and save the raster as:
```
Groundwater_Level_Map.tif
```
  6. Visually inspect the resulting groundwater level surface and verify that the interpolation behaves reasonably in areas with sparse contour coverage.

Correction Using Monitoring Well Data¶

Groundwater contour datasets are typically derived from regional-scale databases and often represent generalized groundwater conditions. Consequently, local deviations may occur, especially in areas influenced by pumping, drainage systems, rivers, or local hydrogeological heterogeneity.

If groundwater monitoring wells with sufficient spatial coverage are available, the groundwater level map should be corrected using observed groundwater levels.

Calculate the average groundwater level for each monitoring well over the selected calibration period.
Extract the interpolated groundwater level from the raster at each monitoring well location.

Calculate the difference between the observed and interpolated groundwater levels:

```text
Error = Observed Groundwater Level − Interpolated Groundwater Level
```

Interpolate the calculated errors to create a continuous correction surface.

Save the correction raster as:

```text
Groundwater_Level_Correction.tif
```

Apply the correction using the Raster Calculator:

```text
Groundwater_Level_Map_Corrected =
Groundwater_Level_Map +
Groundwater_Level_Correction
```

Save the corrected groundwater level map as:

Groundwater_Level_Map_Corrected.tif

This procedure combines the regional information contained in groundwater contour maps with local groundwater observations and often results in a substantially improved representation of the average groundwater conditions.

Limiting Groundwater Levels to the Ground Surface¶

Interpolation and correction procedures may occasionally result in groundwater levels exceeding the terrain elevation in some cells.

For recharge-only applications using the Two-Layer Water Balance method, groundwater levels above the terrain surface may produce unrealistic boundary conditions. Likewise, in fully integrated MIKE SHE models, groundwater levels above the terrain surface may trigger undesired overland flow processes or persistent surface ponding during the initial simulation period.

To avoid these issues while still maintaining high evapotranspiration rates in areas with shallow groundwater tables, it is recommended to limit groundwater levels to a small distance below the terrain surface.

For the Two-Layer Water Balance method, groundwater levels are commonly limited to approximately 5 cm below the terrain surface using the Raster Calculator:

if(
    Groundwater_Level_Map_Corrected > DEM - 0.05,
    DEM - 0.05,
    Groundwater_Level_Map_Corrected
)

where

DEM is the terrain elevation raster.
0.05 m represents a groundwater depth of 5 cm below ground surface.

Save the resulting raster as:

Groundwater_Level_Map_Final.tif

Additional Considerations for Vertically Discretised Unsaturated Zone Models¶

For vertically discretised Unsaturated Zone methods (Richards Equation and Gravity Flow), additional care is required because the groundwater table location determines the coupling between the Unsaturated Zone and Saturated Zone modules.

MIKE SHE ignores Unsaturated Zone nodes located below both the groundwater table and the bottom of the uppermost Saturated Zone layer. Consequently, placing the initial groundwater level too close to the terrain surface may significantly reduce—or even eliminate—the active Unsaturated Zone thickness in some cells.

Whenever possible, it is therefore recommended to position the groundwater table slightly below the bottom of the uppermost Unsaturated Zone cell, or preferably close to the centre of the second Unsaturated Zone layer. This allows

capillary rise to supply moisture to the root zone,
evapotranspiration to remain close to its potential value,
groundwater recharge to be calculated through an active Unsaturated Zone,
stable numerical coupling between the Unsaturated Zone and Saturated Zone modules.

For example, for a vertical discretisation of

0.10 m
0.20 m
0.30 m
0.40 m
...

a suitable groundwater level would typically be located approximately

0.20–0.30 m below ground surface

rather than immediately below the terrain surface.

The exact offset depends on the selected vertical discretisation and the expected groundwater conditions. The general objective is to maintain an active Unsaturated Zone while preserving realistic capillary interaction with the groundwater table.

Export to MIKE SHE Format¶

After completing the final quality control, export the groundwater level map to ASCII Grid format and convert it to DFS2 using the previously described

MIKE Zero Toolbox
└── GIS
    └── Grid2Mike

workflow.

The resulting file

Groundwater_Level_Map_Final.dfs2

can subsequently be used in several different MIKE SHE workflows, including

as the fixed lower boundary condition for recharge-only models,
as an independent validation dataset for steady-state groundwater calibration,
or as the initial groundwater head distribution for transient Saturated Zone simulations.