Open source software for hydrogeologists for mine groundwater management

Dr Robel Gebrekristos

Digby Wells Environmental

Short Course description

There are various software packages used by hydrogeologists for a variety of purposes ranging from project management, database management, data interpretation, conceptual and numerical modelling and decision making. Software is either commercial (produced for sale) or open source (freely available to anyone and for any purpose).

The objective of this course is to promote open source software that can be used by the hydrogeological community to reduce expenses, enhance productivity and maximise efficiency such as in the mining sector.

Free software was previously associated as being inferior in quality in the corporate world. Companies often use commercial software at a hefty price, but little do they know that open source is often equal to, or superior to their commercial counterparts. The source code of open source software can freely be modified and enhanced by anybody. Open source software is a prominent example of open collaboration as it is developed by users for the user community. Companies using open source software do not need to worry about licensing and do not require anti-piracy measures such as product activation or a serial number.


However, the decision of adopting open source software should not just be taken on the basis of the low-cost involved. It should entail a detailed analysis and understanding of the requirements at stake, before switching to open source to achieve the full benefits it offers and to understand what the down side is.

There are plenty of open source products that can be used by hydrogeologists. The packages considered in this short course are those that are frequently used by various specialists in the mining sector and do not necessarily mean that they are the best available. Software gets updated or abandoned with time and what is considered powerful today may be obsolete in a few years.

Some of the well-known open source packages that will be included in the course include: OpenLibre for project management, Blender 3D or Sketchup for 3D conceptual modelling, QGIS for GIS mapping and database management, SAGA GIS for interpolation, PhreeqC for geochemical modelling and ModelMuse for mine groundwater modelling. In addition, there are a number of free software packages developed by the USGS, various universities and consultants across the globe that can be used for aquifer test interpretation, borehole logging and time-series data analysis.


A saving of more than $25,000 can be made per hydrogeologist by utilising such open source packages, while maintaining high quality work that is traditionally completed using commercial software.


There are a number of commercial and open source systems designed to capture, store, manipulate, analyse, manage and present spatial data. It is often thought that high price equals high value and due to this it is always assumed that something paid for is better than something free. But this is not true, especially in this time of the software age.


When considering which GIS software to adopt, two of the most popular choices are ArcGIS and QGIS. ArcGIS is a powerful commercial software, while QGIS is equally powerful tool in the free and open-source software community (Gathu, 2016 and Duggan, 2015).

Since QGIS (Figure 1) is free, there are no licensing concerns. Although ArcGIS is in many ways similar in functionality to QGIS, the problems are linked to copyright protection and the package’s heavy license price.


There are plenty of powerful plugins in QGIS that are tailored for hydrogeologists. Midvatten and Freewat are two examples that are used for hydrological database management and groundwater modelling. In any project, good hydrogeological decisions require good information developed from raw data. The generation and collection of hydrogeological data is expensive, as it requires geophysical surveying, borehole drilling, aquifer testing and other investigations. Data has to be managed in a centralised database if funds are to be used in the most efficient way. This is where Midvatten (displayed in Figure 2) comes handy where point data (such as from boreholes) and linear data (such as geophysical surveys) are all stored in a relational spatialite database.


SAGA GIS (shown in Figure 1) is another open source platform that is powerful in interpolation and terrain analysis. It contains a number of interpolation algorithms including kriging. Although SAGA GIS can be used as a standalone package, it is also a QGIS plugin.

Maps produced using free GIS software QGIS
Maps produced using free GIS software SAGA GIS

Figure 1. Maps produced using free GIS software QGIS (left) and SAGA GIS (right)

Figure 2. Structure of the hydrogeological database management system of Midvatten (QGIS plugin)
Figure 2. Structure of the hydrogeological database management system of Midvatten (QGIS plugin)

Figure 2. Structure of the hydrogeological database management system of Midvatten (QGIS plugin)


Three dimensional (3D) conceptual modelling is the process of creating a 3D representation of any surface of an object by manipulating polygons, edges, and vertices. 3D visualisation is not new. Geologists have illustrated their data with 3D drawings and models for centuries (Kresic and Mikszewski, 2013). What has changed are the tools. What was once pen and ink, are now geospatial visualisation techniques that allow for the rapid  generation of hundreds of multidimensional views of a site, animated over multiple parameters digitally, and distributable in an interactive format.

3D methods can improve subsurface depictions of hydrogeological settings, which is useful in groundwater projects. Hydrogeologists now work with innovative technologies designed to capture and assimilate vast amounts of geospatial site data, and to render the data into interactive 3D visualisations. This is now possible due to technology advances in digital cartography, GIS, data storage, analysis, and visualization tools.

An expanding assortment of visualisation software is available to address the needs of the working hydrogeologist (Kresic and Mikszewski, 2013). Choosing the best modelling software is often difficult because of various aspects and wide range of features available in these tools. Blender 3D and Sketchup, are some of the top examples of free computer programmes for 3D hydrogeological visualisation. Screen shots of 3D models of a coal and platinum mines modelled in Sketchup are illustrated in Figure 3 and Figure 4.

Figure 3. 3D model of a defunct coal mine flooding using Sketchup
Figure 4. 3D model showing a cone of dewatering at a platinum mine using Sketchup

Figure 3. 3D model of a defunct coal mine flooding using Sketchup

Figure 4. 3D model showing a cone of dewatering at a platinum mine using Sketchup


After the hydrogeological characterization of the site has been completed and the conceptual model developed, software is selected to solve the groundwater issue numerically. While groundwater models are, by definition, a simplification of a more complex reality, they have proven to be useful tools over several decades for addressing a range of groundwater problems and supporting the decision-making process.

Numerical modelling has become an important methodology in support of the planning and decision-making processes of groundwater management (Kumar, 2012). Groundwater models play an important role in the development and management of groundwater resources, and in predicting effects of human-induced stresses. There are many different groundwater modelling codes available, each with their own capabilities, operational characteristics, and limitations.

ModelMuse (Figure 5) is the most prominent open source groundwater modelling graphical user interface developed by U.S. Geological Survey (USGS) (Winston, 2014). ModelMuse accommodates MODFLOW-2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM, MT3DMS, SUTRA, PHAST, MODPATH, and ZONEBUDGET.


MODFLOW-2005 is a three-dimensional finite-difference groundwater model. It simulates steady and non-steady flow in an irregularly shaped flow system in which aquifer layers can be confined, unconfined, or a combination of confined and unconfined. MODFLOW-LGR adds local grid refinement to MODFLOW. MODFLOW-NWT provides an alternate method for solving problems involving drying and rewetting nonlinearities of the unconfined groundwater-flow equation. PHAST simulates multi-component, reactive solute transport in three-dimensional saturated groundwater flow systems. SUTRA is a finite-element simulation model for saturated-unsaturated, fluid-density-dependent ground-water flow with energy transport or chemically-reactive single-species solute transport.

Figure 5. ModelMuse GUI for finite difference (left) and finite element (right) modelling
Figure 5. ModelMuse GUI for finite difference (left) and finite element (right) modelling

Figure 5. ModelMuse GUI for finite difference (left) and finite element (right) modelling


PHREEQC is a free computer program developed by USGS (Parkhurst & Appelo 2013) for simulating chemical reactions and transport processes in natural or polluted water, in laboratory experiments, or in industrial processes. The program is based on equilibrium chemistry of aqueous solutions interacting with minerals, gases, solid solutions, exchangers, and sorption surfaces, which accounts for the original acronym—pH-REdox-EQuilibrium, but the program has evolved to include the capability to model kinetic reactions and 1D (one-dimensional) transport.

Rate equations are completely user-specifiable in the form of Basic statements. Kinetic and equilibrium reactants can be interconnected, for example, by linking the number of surface sites to the amount of a kinetic reactant that is consumed (or produced) in a model period. A 1D transport algorithm simulates dispersion and diffusion; solute movement in dual porosity media; and multicomponent diffusion, where species have individual, temperature-dependent diffusion coefficients, but ion fluxes are modified to maintain charge balance during transport.

A powerful inverse modeling capability allows identification of reactions that account for observed water compositions along a flowline or in the time course of an experiment. Extensible chemical databases allow application of the reaction, transport, and inverse-modeling capabilities to almost any chemical reaction that is recognized to influence rainwater, soil-water, groundwater, and surface-water quality.

An example of a PhreeqC geochemical model is illustrated in Figure 6 (after Parkhurst & Appelo 2013). It shows a result of transport simulation of the chemical evolution of groundwater due to calcium magnesium bicarbonate water inflow to an aquifer initially containing a brine, calcite and dolomite, a cation exchanger, and a surface that complexes arsenic.

Figure 6. Transport and chemical evolution modelling using PhreeqC in groundwater (Parkhurst & Appelo 2013)

Figure 6. Transport and chemical evolution modelling using PhreeqC in groundwater (Parkhurst & Appelo 2013)


It is difficult for a team of hydrogeologists that have to handle multiple projects to rely on human memory to keep their projects organized. To deliver projects on time and within budget, information needs to be written down, deadlines plotted, and documents shared. The solution for successful management of big projects is to use project management software.

Project management software has the capacity to help plan, schedule and organise resources. There are numerous desktop and browser based project management software which can be used in the management of hydrogeological projects. One of such product is ProjectLibre which is a leading open source alternative to Microsoft Project. ProjectLibre is compatible with Microsoft Project 2003, 2007 and 2010 files. A screen shot of a project scheduled in ProjectLibre is shown in Figure 7

Figure 7. Project scheduling and resource allocation prepared in ProjectLibre
Figure 7. Project scheduling and resource allocation prepared in ProjectLibre

Figure 7. Project scheduling and resource allocation prepared in ProjectLibre


Duggan, N (2015) “QGIS vs ArcGIS”

Gathu, J (2016) “Which software is better: QGIS or ArcGIS?”

Kresic, N and Mikszewski, A (2013) “Hydrogeological Conceptual Site Models: Data Analysis and Visualisation”.

Kumar, CP (2012) “Groundwater Modelling Software – Capabilities and Limitations”.

Parkhurst DL, Appelo CAJ (2013) User's guide to PHREEQC (Version 3) -- a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations.- U S Geological Survey Water-Resources Investigations

Winson, RB (2014) “Modifications Made to ModelMuse to Add Support for the Saturated-Unsaturated Transport Model (SUTRA)

Date: July, 14, 2019

Minimum: 5 delegates,

Maximum: 15 delegates


  • Regular €250/€270,

  • Students €170/€200