Teaching & Supervision

Of Karst! – short episodes about karst

Of Karst! – short episodes about karst

Episode 2: Dissolving rock? (or, how karst evolves).

Post by Andreas Hartmann, Lecturer in Hydrology at the University of Freiburg (Universität Freiburg), in Germany. You can follow Andreas on twitter at @sub_heterogenty.

Didn’t get to read Episode 1? Click this link here to do so!


In the previous episode, I introduced karst by showing how it looks in different regions in the world. This episode will now deal with the processes that create such amazing surface and subsurface landforms. The widely used term “karstification” refers to the chemical weathering of easily soluble rock composed of carbonate rock or gypsum. Most typical is karstification of limestone (consisting of the mineral calcite, CaCO3) or dolostone (consisting of the mineral dolomite, CaMg(CO3)2). If exposed to CO2 rich water these rocks are dissolved to form aqueous calcium (Ca2+) or magnesium (Mg2+) and bicarbonate (HCO3 ) ions. For calcite, karstification is described by the following chemical equilibrium:

The dissolution of carbonate rock depends on various factors. Imagine a solid block of salt, which you pour water on. If completely solid, the water will flow down the salt surface slowly dissolving the block. If fractured, water will eventually enlarge the fractures in the salt block and dissolution will occur much faster. Now imagine smashing the salt block before pouring water on it. In such circumstances the salt will dissolve even faster as the surface area exposed to the water is much larger.

Karst and its evolution (educational video provided by Jennifer Calva on Youtube).

The same is true for karstification. If the carbonate rock is heavily fractured, it will dissolve faster than unfractured carbonate rock. Another factor is the availability of CO2, that depends on the relative amount of CO2 in the air, air temperature and soil microbiotic processes. Other factors are the purity of the carbonate rock, the availability of water, and the supply of CO2 from the surface. As soon as karstification takes place, more water will be able to pass the dissolution enlarged fractures providing more and more CO2, and creating a positive feedback between rock dissolution and water flow:

Positive feedback between carbonate rock dissolution and water flow (Hartmann et al., 2014, modified).

The hydrochemical processes described in this episode of the Of Karst! Series not only create beautiful karst landscapes but they also have a strong and particular impact on water flow paths in the subsurface, which will the topic of episode 4 that can be expected in early 2018. Before, I will present a special feature about karst in the movies as topic of episode 3 in autumn 2017.

Further reading

Hartmann, A., Goldscheider, N., Wagener, T., Lange, J. & Weiler, M. 2014. Karst water resources in a changing world: Review of hydrological modeling approaches. Reviews of Geophysics, 52, 218–242, doi: 10.1002/2013rg000443.

Ford, D.C. & Williams, P.W. 2013. Karst Hydrogeology and Geomorphology. John Wiley & Sons, 576 pages.




Andreas Hartmann is a lecturer in Hydrology at the University of Freiburg. His primary field of interest is karst hydrology and hydrological modelling. Find out more at his personal webpage www.subsurface-heterogeneity.com.


Groundwater & Education – Part One

Groundwater & Education – Part One

Post by Viviana Re, postdoctoral researcher at the University of  Pavia (Università di Pavia), in Italy. You can follow Viviana on Twitter at @biralnas.

Part one of a two part series on groundwater and education by Viviana.


Education /ɛdjʊˈkeɪʃ(ə)n
The process of receiving or giving systematic instruction, especially at a school or university.

  • from Latin educatio(n-), from the verb educare
  • Educare is a combination of the words e (out) and ducare (lead, drawing), or drawing out.

Based on this definition, I should change the title of this post to: Drawing out groundwater (from the well). This is actually the main occupation of groundwater scientists, isn’t it? Not only are we always withdrawing groundwater from a well or a borehole while sampling, but we also often have to “draw it out” when dealing with managers and policy makers, as sometimes they seem to forget about this hidden (but very important) component of the water cycle. Therefore, we are quite used to these forms of “drawing out” – but what about education? Are we really that effective in “drawing out” groundwater in explaining its peculiarities, issues, and connections within the whole water cycle and, more generally, with the environment?

Indeed, the effort of shedding light on something that is not so visible nor easily studied has the side effect of forcing us to focus solely on it, with a resulting tendency of developing sectorial approaches to water management.

In the preface of a UNESCO Technical paper, I found the following excerpt: “Water resources schemes are now increasingly considered as integrated systems and consequently, civil engineers, geologists, agricultural engineers and hydraulic engineers engaged in planning and design no longer work in isolation”. The document is dated 1974 but, still in 2017, we are somehow struggling to fitting groundwater into Integrated Water Resources Management (IWRM) and to connecting mental and structural “silos”. Quoting Daly (2017), the latter is particularly relevant (especially when education is at stake): if on the one hand, specialization can be the driver for a sound knowledge; on the other hand, this can encourage people to get stuck in their own individual disciplines (or said in other words, their “silos”). Indeed, “silos” exist in their structures, but can also exist as a state of mind that can go hand in hand with tunnel vision (Tett, 2015).

Therefore, in my opinion, the new generation of groundwater scientists (and teachers) should have a new mission: to work (and therefore, to teach) coherently with the integrated and complex nature of the water cycle. In fact, the role of hydrogeologists and groundwater scientists in times of increasing freshwater demand, exacerbated by population growth and climate change effects, requires a serious shift towards a more holistic approach targeting sound groundwater assessment and long-term management.

Arguably, if we are still discussing possible ways of practically implementing this integration, we should definitely start asking ourselves if the the “business as usual” way of working and teaching is effective.  If it is not, we must begin investigating how we can go beyond classical approaches to draw groundwater out of the well.

Playing with kids while sampling … can we call it capacity building?!


To be continued …

[Read More]

Research mini-conference in fourth year groundwater class

Research mini-conference in fourth year groundwater class

Fourth year and graduate students led a fun mini-conference during class in Groundwater Hydrology (CIVE 445, Civil Engineering at University of Victoria) yesterday. Local consulting and government hydrogeologists joined, making the students both nervous and excited to be presenting to professionals with up to forty years of groundwater experience. The presentations were the culmination of a term-long independent group research project – they also write a research paper (which is peer-reviewed by their classmates). And the mini-conference culminated in beers at the grad club, unfortunately drinking beer brewed with surface water.

It seemed like a win-win-win for everyone. The students loved meeting and presenting to, and being grilled by, the people who had mapped the aquifer they were modeling or asked if their model is based on any real data. The practitioners loved seeing the new ideas and enthusiasm of the students. And I loved seeing the interaction and learning.

For any prof reading this, here is a description of the Group Research Project and the conference poster:






What is a hydrogeologist?

What is a hydrogeologist?

Hydrogeologists are a diverse group, in part because we come to this discipline from so many different paths.  We come from different academic programs in engineering, geological sciences and environmental sciences.  These differences in backgrounds create a diversity of perspectives, which enriches hydrogeology and allows for dynamic collaborations.  Engineers and geophysicists are known for bringing quantitative skills to hydrogeology, while geologists shine in problems involving stratigraphy, structural geology and embrace uncertainty.  Geochemists and environmental scientists are often stronger in contaminant hydrogeology.  However, each of these backgrounds also have their deficiencies.  This is underscored by looking at programs in civil engineering and geology, which are two of the most common undergraduate degrees among hydrogeologists. Aside from foundational math and science courses the first years of these programs, they usually only share an elective course in hydrogeology.  A review of hydrogeology courses covered by Gleeson et al. (2012)  showed that aside from a few topics, these courses vary substantially in their content.


Hydrogeologists are often found crossing streams wearing ghost-buster backpacks (or so it seems from here)

This is further complicated by how professionals are licensed in many jurisdictions, which is often based on these academic programs rather than whether someone has the capacity to practice hydrogeology.  Engineers are required to have engineering fundamentals in areas such as statics, dynamics, and engineering design, along with competency is areas such as structural and transportation engineering for civil engineering. Geologists receive professional registration based on core competencies in subjects such as mineralogy, sedimentology, paleontology and structural geology.  Registration for fields more closely aligned with hydrogeology, such as environmental geoscience and geological engineering may consider hydrogeology as a core requirement.  In general, this means that somebody registered as a professional engineer or geoscientist might be a hydrogeologist but they also may have very little knowledge of hydrogeology.  Environmental scientists and similar fields might be better prepared to practice hydrogeology in some instances but professional registration is not as common.

Maybe this involves graduate school?  Many practicing hydrogeologists have advanced degrees.  These programs are often designed to give a broad base in hydrogeology and typically deliver material in:

  • physical hydrogeology
  • chemical/contaminant hydrogeology
  • geochemistry
  • numerical modeling
  • field techniques

Additional material on porous media, geotechnical engineering and hydrology are frequently also covered.  Anyone with a background in these areas is probably a hydrogeologist.  However, there are still some grey areas.  Can someone who doesn’t understand numerical models be a hydrogeologist? What about someone who has never done field work?  Where to draw the line is unclear and may differ substantially based on who is asking the question.  However, if the goal is to promote competent practitioners and researchers in hydrogeology, the traditional paths through engineering and geoscience may be less than ideal.  The requirement of knowledge outside hydrogeology at the expense of core knowledge may be holding us back. On the other hand, a great number of us did not enter university with the goal of becoming a hydrogeologist and maybe we need these more traditional programs as gateways.

What most hydrogeologists working really looks like (from here)

Water Underground has a new home on the EGU Network Blogs

Water Underground has a new home on the EGU Network Blogs

The newest addition to the Network Blogs is a groundwater nerd blog written by a global collective of hydrogeologic researchers for water resource professionals, academics and anyone interested in groundwater, research, teaching and supervision.

Water Underground was started, and is currently led, by Tom Gleeson. It is the first blog to be jointly hosted by the EGU Blogs and the AGU blogosphere.

Why not take a look at some the past posts to get a feel for what is to come on the new EGU/AGU blog? You can read about what stalagmites can teach us about past and present climate and what scientists mean by crustal permeability. The advances in groundwater research also feature on the blog. Posts on supervision and teaching will be of interest to Earth scientists at all stages of their career too.

Posts in the blog are contributed by a collective of hydrology experts and reviewed by one of the frequent contributors to help improve style and clarity. Tom, and the contributing authors, want to foster a lively community via the blog, so discussion as well as comments on posts is encouraged. Not only that, if you have something to share, be sure to contact the editorial team as submissions are always welcome! Simply drop them a line at: waterundergroundblog@gmail.com

Here at EGU we are thrilled to have Water Underground join our diverse community of geoscience bloggers. Please join us in welcoming Water Underground to the Network Blogs!

By Laura Roberts,  EGU Communications  Officer

FloPy: A Python interface for MODFLOW that kicks tail!

FloPy: A Python interface for MODFLOW that kicks tail!

Authored by: Kevin Befus – Assistant professor, Department of Civil and Architectural Engineering at the University of Wyoming

Groundwater modeling is getting better. Models are becoming more sophisticated with simpler interfaces to add, extract, and process the data. So, at first appearances, the U.S. Geological Survey’s (USGS) recent release of a Python module named FloPy for preparing, running, and managing MODFLOW groundwater models seems to be a step backwards.

Oh, but it isn’t.


First, a couple disclaimers. Yes, at the time of writing this I work for the USGS and use this new Python module for my research. Did I have to use FloPy? No. Am I glad I did? YES! Before using FloPy, I dabbled in the various non-commercial MODFLOW interfaces but got bogged down on how many drop down menus, pop-up menus, wizards, and separate plotting programs with their own menus were needed to make a meaningful groundwater model on top of a new lexicon of variable names (IUPWCB must mean “internally unknown parameter with concentrated bacon”, right?).

FloPy made its official debut in February 2016 with a Groundwater methods report 1. Bakker et al. do an excellent job telling us why we should use FloPy. I’ll leave that to you and tell you what I think.

Here’s what is great about FloPy:

  1. FloPy is 100% MODFLOW. No tweaks to anything. You choose the executable file you want it to use or compile it yourself, and you’re off!
  2. You have the near-infinite data management, manipulation, and plotting capabilities of Python at your fingertips. Python has a lot of packages. It can be overwhelming. You can rely commercial packages like ESRI’s arcpy if you want, but there’s a list of free libraries that give you even more freedom to get the input data just right. Since I mentioned freedom, here’s the list of free libraries I find useful but it is in no way an endorsement nor exhaustive: scipy, numpy, gdal, osgeo, fiona, shapely, cartopy, pyshp, pandas, matplotlib, and let’s not forget…flopy!
  3. It’s easy to duplicate and alter an existing model. Once you have your script perfect for running a particular groundwater model, you can take pieces of it to make a slightly altered version, or you can pop it in a loop that runs through your uncertain inputs for sensitivity testing. Change your grid with the flip of a variable, and make sure that mesh converges!
  4. Loading other MODFLOW models works great. Say you want to run someone else’s model with slightly different recharge, but their recharge is variable in space. Since FloPy incorporates numpy’s grid/matrix handling capabilities, you can change individual entries with row-column selections or change the whole recharge grid by multiplying it by either a single number or say a random matrix with a normal distribution and some added noise. If you just want to use their recharge data to run your own model, you can save the position coordinates (they have hopefully provided you with their coordinate system and model transformations) and recharge arrays to your very favorite format (csv, nc, mat, tif) and load it later as a matrix to add to your model, all in a single Python script.
  5. Building off of the ability to load or create MODFLOW models, FloPy has functions for plotting 2D map or cross-section views of the model discretization, boundary conditions, and results. Shapefiles can be included in these plots if they are in the same coordinate system as the model or extracted from the model (ever want a polygon feature of every model cell with attributes for every property of that cell?). I do my own shapefile manipulations in Python, but FloPy has some great plotting tools built in.
  6. You already have the data in Python. See what adding a low permeability layer does to spring discharge. Then, with the model made, you have to make sense of it. Maybe develop some interesting spatial or time series analyses. Enter Python. Plotting with matplotlib also makes beautiful, journal article-worthy figures…with enough sweat and tears from your end (not as many as you may think). Yes, this is a repeat of 2), but, seriously, it’s in PYTHON!
  7. FloPy is totally free. Python is free. Tons of science-oriented libraries in Python are free.


Here’s a flashy example.  It is straightforward and only takes one script to create a SEAWAT model from scratch and plot the 2D steady state salinity distribution and flow vectors for a simple Henry 2 problem based on a slightly edited FloPy example script.  There are more than a dozen example scripts available on the FloPy site as well as a very cool capture ratio script provided in the methods report 1.

For the groundwater educators out there, a FloPy groundwater model script can be paired with homework questions that get students testing how changing hydraulic conductivity in certain parts of the model changes the water table configuration. Or maybe a new well needs to be drilled on a plot of land near a spring… The scenarios are endless. Students can develop a fundamental understanding of groundwater flow while getting experience with both groundwater modeling and computer programming. Win, win, and win.

Essentially all of the standard MODFLOW packages are operational in FloPy, and there are varying levels of support for some of the specialized MODFLOW compilations and processing tools (e.g., MODFLOW-USG, MODFLOW-NWT, MT3DMS, SEAWAT, PEST, and MODPATH). PEST and MODPATH are currently not executable with FloPy, but these features will probably be added in a future release (I have made my own klugy modules for running ZoneBudget and MODPATH that interface reasonably well with the rest of FloPy).

Get on your way and give FloPy a try today!


The Python package is available online at https://github.com/modflowpy/flopy.

The documentation is available online at http://modflowpy.github.io/flopydoc/index.html.

The USGS FloPy page is http://water.usgs.gov/ogw/flopy/.


Bakker, M., V. Post, C. D. Langevin, J. D. Hughes, J. T. White, J. J. Starn, and M. N. Fienen (2016), Scripting MODFLOW Model Development Using Python and FloPy, Groundwater, doi:10.1111/gwat.12413.

Henry, H.R., 1964. Effects of dispersion on salt encroachment in coastal aquifers. In: Cooper, H.H. (Ed.), Sea Water in Coastal Aquifers: U.S. Geological Survey Water- Supply Paper 1613-C p. C71–C84.

About the author:

Kevin Befus is a groundwater hydrologist with geology and geophysics experience — examining geological, biological, and chemical processes, especially considering their connections to water across scales.


One hell of a great groundwater textbook now available free

One hell of a great groundwater textbook now available free

‘Groundwater’ the seminar text book from Freeze and Cheery (1979) is free in pdf now…just follow the links here. This text book is almost as old as I am and important parts of modern hydrogeology are rusty or non-existent (like hydroecology amongst other topics) but it is still lucidly written and useful.  I routinely send students to read chapters so I am happy that it is now available free.

Kudos to Pearson Publishing, Alan Freeze and John Cherry and Hydrogeologists without Borders! I look forward to Groundwater2.0 which is in the works!



The new and exciting face of waterunderground.org

The new and exciting face of waterunderground.org

by Tom Gleeson

I started waterunderground.org a few years ago as my personal groundwater nerd blog with the odd guest post written by others. Since I love working with others, I thought it would be more fun, and more interesting for readers, to expand the number of voices regularly posting. So here is the new face of the blog…


a kind of weird image of collective action

What is the new blog all about?

Written by a global collective of hydrogeologic researchers for water resource professionals, academics and anyone interested in groundwater, research, teaching and supervision. We share the following aspirations:

  • approachable groundwater science at the interface of other earth and human systems
  • encourage sustainable use of groundwater that reduces poverty, social injustice and food security while maintaining the highest environmental standards
  • compassionate, effective supervision
  • innovative, effective teaching
  • transparency of scientific methods, assumptions and data

Check out more details and how to be part of the blog on about.

Frequent contributors include:

  • Andy Baker (University of New South Wales, Australia) – caves and karst (I actually visit the water underground!), climate and past climate
  • Kevin Befus (University of Wyoming, United States) – groundwater-surface interactions, coastal groundwater, groundwater age
  • Mark Cuthbert (University of Birmingham, United Kingdom) – groundwater recharge & discharge processes, paleo-hydrogeology, dryland hydro(geo)logy, climate-groundwater interactions
  • Matt Currell (RMIT University, Australia) – isotope hydrology; groundwater quality; transient responses in aquifer systems
  • Inge de Graaf (Colorado School of Mines, United States) – global groundwater withdrawal, flow and sustainability
  • Grant Ferguson (University of Saskatchewan, Canada) – groundwater & energy, regional groundwater flow, sustainability
  • Tom Gleeson (University of Victoria, Canada) – mega-scale groundwater systems and sustainability
  • Scott Jasechko (University of Calgary, Canada) – global isotope hydrology; groundwater, precipitation, evapotranspiration
  • Elco Luijendijk (University of Gottingen, Germany) – paleo-hydrogeology,deep groundwater flow,large scale groundwater systems
  • Sam Zipper (University of Wisconsin – Madison, United States) – ecohydrology, agriculture, urbanization, land use change

Making guidelines for graduate students

Making guidelines for graduate students

I strive for effective, compassionate supervision and I clarify my goals, approach and expectations in my guidelines for graduate students (available here, from McGill’s best practices in supervision). As I wrote, most students enter a relationship with a thesis advisor without a clear idea of what they can expect so I compiled this handout to give you some idea of what I expect of you as student and what you can expect of me as an advisor. So that this never happens, I hope:


My highest level priority is for both of us to communicate and set mutually-agreed-upon goals (LINK OTHER POST) and then both do our best to make those goals into reality. As one of my students, I plan to treat you as a junior colleague who is maturing into a professional engineer or scientist. This means that you can actively co-create opportunities to meet your goals, and also puts a large responsibility on your shoulders to live up to the expectations of performance that are required of a colleague.

I have found clarifying my goals, approach and expectations in my guidelines for graduate students have helped students and helped me be a more effective and compassionate supervisor.

Thank you to the awesome Cutting Edge Workshop for Early Career Geoscience Faculty where I learned about graduate student guidelines a few years ago. I emphatically encourage all young faculty to attend!

How to peer review: skill-building in a grad classes

How to peer review: skill-building in a grad classes

I teach how to peer-review in graduate class because I think it is a core skill for any professional.  I first demystify peer-reviewing and academic journals, and answer questions that all students have about these topics that they have heard about but rarely learn about using this:

peer review

Nicholos and Gordon EOS, 2011

I describe my personal experience as a manuscript submitter, reviewer and associate editor. And then I outline the structure and types of questions to ask during a peer review (both listed below), and challenge them with three, increasingly difficult steps to learn how to peer review:

  • first, peer review already published papers (which is surprisingly hard since it is already well edited but this is useful as practice and since it is impersonal).
  • Second, peer review an open access manuscript that is currently in review (i.e. HESSD  or other open access journal). These can be actually submitted to the journal or not.
  • Third, they peer-review eachother`s term papers before final submission of paper to me as part of the grade.

At each step myself or a TA gives them feedback and evaluates their peer reviews.

Good structure for a peer-review

  • Short summary (1-2 sentences) and general assessment of novelty/contribution. Give the author(s) a few compliments here….everyone likes to eat the good-bad-good sandwich rather than just the bad sandwich.
  • Discuss major concerns or suggestions for authors. Aim for positive criticism here.
  • Recommend course of action: reject, accept with major revisions or accept with minor revisions.
  • Document minor concerns with explicit page and line numbers.

Good questions to ponder:
Contributions and Audience:
What are the important contributions of this paper?
Does the paper make a significant, new contribution to this research area?
Who is the intended audience?

Technical soundness:
Are the methods fully described?
Is the mathematical/theoretical development (if any) complete and accurate?
Is the approach, experimental design, review or statistical analysis appropriate?

Organization and Style:
Is the paper a description of an experiment or concept or a synthesis of previous work?
Is the paper well written and organized?
What is the hypothesis, objectives or goals put forth?Are all the tables and figures necessary?
Can the paper be shortened?

Are the interpretations of data and results justified?
What are the major conclusions? Are they significant? Are they interesting? What remains answered?

Your reactions:
Did you gain something from the paper (be specific)?
How does the paper relate to other topics discussed in class?Are such questions and/or methods relevant to your own research?


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