Modeling Groundwater Chemistry with PHREEQC, PHAST and Python

(1 customer review)

50 hours / 6 weeks

Online course

Dates: 12th October – 23rd November

Standard Unemployed Or Student
290 190


Geochemical speciation modeling, based upon chemical thermodynamic relationships between aqueous species, mineral phases, and gases in closed as well as open systems, can be used to study a large variety of problems in earth and environmental sciences. A random sampling of topics includes ore formation processes, petroleum reservoir or playa lake brine chemistries, soil pedogenesis, geologic storage of hazardous and radioactive wastes, and the environmental chemistry of shallow aquifer environments, the latter potentially including trace element mobility, bioremediation, and agricultural/nitrate impacts. Geochemical models simulate reactions in such systems by solving mass-, charge-, and valence electron-balance equations among the relevant species and components, constrained by databases of equilibrium constants. These reaction modeling capabilities can be extended to include irreversible reactions, water-rock and water-gas mass exchanges, reaction kinetics, solid solution chemistry, and other phenomena.

Geochemical models can be used in a “batch” or zero-dimensional mode to simulate a variety of scenarios, such as mixing of two solutions with different chemistries, equilibration of water chemistry with a mineral assemblage, or the geochemical response of a water + mineral assemblage + gas system to the addition of one or more external reactants (e.g., a waste package, or an additive to promote changes in oxidation-reduction conditions for remediation of a contaminated site). In addition, a geochemical model can be used as a component of a more complex, multi-dimensional reactive transport model, where dissolved constituents are transported from one location to another in response to hydraulic gradients and diffusion, while subject to spatially-variable chemical reaction processes.

An understanding of geochemical and reactive transport modeling, using well-vetted simulation packages available in the public domain, will provide practicing hydrogeologists with a capability to quantitatively explain, and predict, the chemical evolution of aquifer environments in a variety of contexts.

Course objectives

This course will provide practical instruction in the use of PHREEQC and PHAST, two public-domain models available for download from the United States Geological Survey, to simulate aqueous geochemical processes and reactive transport in groundwater systems. After the key concepts for understanding and running both models are covered, techniques for extending the applicability of both packages using Python will also be explored.

At the conclusion of the course, students will be able to:

  • Construct PHREEQC simulations for a variety of situations, including water-rock and water-gas systems, reactions involving mineral surfaces (ion exchange, surface complexation), and oxidation-reduction processes. Students will also understand how to apply more complex features, such as using solid-solution formulations for variable-composition mineral phases, and how to implement reaction kinetic expressions in a model.
  • Construct PHAST simulations of multispecies reactive transport in groundwater, including systems entailing hydrologic as well as geochemical/mineralogical heterogeneities.
  • Use Python scientific programming tools, together with PHREEQC and/or PHAST, to address additional problems; examples will include reactive transport through partially-saturated porous media and conducting sensitivity analyses to parameter values. Also, Python scripts to process model input (e.g., specifying mineral assemblages) and output (e.g., Stiff diagrams) will be developed.

The course will be presented through the use of multimedia explanatory exercises, instructional videos, and a webinar involving working through a specific PHAST application for an environmental remediation example problem.

Limited places.

The instructional modules which will be covered in this course will include, in sequence:

  • – Module 1. Introduction to aqueous geochemical modeling: key principles, types of potential applications, and practical limitations.
  • – Module 2. Working with PHREEQC: program installation, simulator capabilities and limitations, user interface and keyword block organization, supplied thermodynamic and partitioning coefficient databases.
  • – Module 3. Example PHREEQC applications: starting with simple aqueous speciation problems, applications with increasing complexity will be introduced, including oxidation-reduction reactions, temperature- and pressure-dependent reactions, systems featuring irreversible reactions, and reaction kinetic expressions for mineral dissolution reactions.
  • – Module 4. Introduction to reactive transport modeling with PHAST: review the finite-difference method for solving flow and transport equations for porous media, set up two-dimensional reactive transport models with keyword blocks, including assigning initial conditions, mineral equilibration reactions, and boundary conditions.
  • – Module 5. Building complex groundwater reactive transport models with PHAST: explore setting up, running, and visualizing various example applications, including acid mine drainage, assessing groundwater impacts stemming from agricultural operations discharges, and heavy metal remediation.
  • – Module 6. Using Python to support and enhance PHREEQC and PHAST model development: brief overview and review of Python scripting, processing model input and output (including generation of PHAST models with physical and geochemical/mineralogical heterogeneities), and, as a challenge exercise, develop a rudimentary one-dimensional reactive transport model for a variably water-saturated soil column (using numerical tools available in the Scipy scientific library for Python).

Walt McNab

Walt McNab is a hydrogeologist with almost 30 years of professional experience, including roles as a research scientist with Lawrence Livermore National Laboratory, California, USA, and as a consultant for environmental and water supply projects. His primary interests involve simulation of flow, transport, and chemical processes in groundwater and soil systems, and scientific programming to support quantitative data analysis and development of customized simulation tools using Python and Julia. His modeling expertise includes geochemical/reactive transport models (PHREEQC/PHAST), groundwater flow (MODFLOW), flow and transport through unsaturated soils (HYDRUS, VS2DT), as well as multiphase flow through porous media (custom-developed simulation tools). He holds a Ph.D. from the University of California, Berkeley, and is a registered Professional Geologist in California, USA.

Within this virtual platform, students are in continuous contact with professor in a tailored way, solving questions together, and widening knowledge and acquiring new skills. Students can also interact with other students and professors through webinars and forums.

This course is aimed at hydrogeologists as well as environmental engineers and scientists with some previous exposure to water chemistry concepts (e.g., familiarity with major cations and anions typically measured in groundwater, alkalinity, pH, redox) and a general understanding of the mineralogy encountered in various types of aquifer environments. Knowledge of basic flow and transport concepts for saturated and partially-saturated porous media is assumed. The course will also require some familiarity or experience with numerical groundwater models (e.g., MODFLOW/MT3D) as well as Python scripting. Access to visualization software (e.g., commercial packages such as Surfer, or open-source equivalents) would be helpful, but not required.


As evidence of knowledge gained throughout the course, a certificate will be issued from the Virtual platform. This certificate is based on the modern technology Blockchain, which increases security, prevents fraud, builds trust and ensures you’re ready for the future.

Familiarity with geochemical modeling is an advantageous skill for practicing hydrogeologists, with an understanding of reactive transport modeling representing an additional level of specialization that will enable contribution to many challenging, complex environmental problems. Separately, knowledge of Python scripting to augment model pre- and post-processing is a key, in-demand skill for a wide range of professional scientific and engineering fields.

1 review for Modeling Groundwater Chemistry with PHREEQC, PHAST and Python

  1. Essam Alwagdani

    I found through Ingeoexpert an online course that I was looking for a long time. It is rarely available online.

    The course was very specialized, nicely organized, and highly beneficial.

    It was very great; keep going.

    Thank you so much

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