June 06, 2022

River-Well-Aquifer Geospatial Groundwater Flow Model with Voronoi Mesh - Tutorial

June 06, 2022/ Saul Montoya

This is an applied example of a fully geospatial groundwater flow model with the MODFLOW 6 Disv discretized by vertices option. Model was constructed with Python and Flopy from a series of shapefiles and it has a progressive refinement for well and river boundary conditions. Regional flow has been simulated as a General Head Boundary and plotting options were developed for the grid and model output representation on areal view and cross section.

October 04, 2021

New website! MODFLOW Questions and Answers: ask anything on groundwater modeling

October 04, 2021/ Saul Montoya

Until now we had limited options to provide specific support in groundwater modeling. We know that modeling requires the review of extensive documentation and practical work with the software and sometimes or most times we don't have the time to sort things out.

September 15, 2021

Example of Seawater Intrusion Modeling with Modflow 6, Model Muse and Flopy - Tutorial

September 15, 2021/ Saul Montoya

MODFLOW 6 implements the Buoyancy package for the simulation of variable density and seawater intrusion cases. The tools are implemented in the Python package Flopy, however the workflow has changed substantially from the previous models of flow and transport. We have developed an applied case seawater intrusion model on a regular geometry model constructed with Model Muse for flow and Flopy for transport.

August 23, 2021

What to do when your MODFLOW MT3D contaminant plume doesn’t migrate?

August 23, 2021/ Saul Montoya

This is a problem that every hydrogeologist - numerical modeler has faced many times over his/her professional career independently from the theoretical background and skills with the code, graphical user interface or Python library.

We don’t know why groundwater “flows” and a contaminant plume “migrates” when both move on the aquifer system. After you construct you model geometry, setup the flow boundary condition, specify your transport package, define your contaminant sources, run your MODFLOW flow model and then run your MT3D model (or even your MT3DMS model) you will find that there is no plume, none, nada, nichts.

August 16, 2021

Is glTF an alternative to VTK for the representation of voronoi mesh Modflow6 models?

August 16, 2021/ Saul Montoya

Representation of geospatial objects in 2D are well covered by the GIS software and standards where we have powerful tools and interchangeable spatial files, however when we work on 3D objects the universe of software and tools is like a jungle with a wide variety of issues. We will always consider 3D as the ultimate representation of an object using a computer, by sure the holograms and augmented reality can improve the way we interact with a object geometry, but since we are not in the common near future we will give much effort to the representation of these objects in our computer screens, tables and cellphones.

July 02, 2021

How to insert and read Observation Points (OBS6) in Modflow 6 with Model Muse and Flopy - Tutorial

July 02, 2021/ Saul Montoya

Modflow 6 has a new approach in setting up observation points and it's essentially different to the previous versions. The OBS6 package works not only with heads and drawdowns but also with flows, so it's also possible to calibrate the model against baseflow or any other recorded flow from a boundary condition directly. We have created an applied case of the implementation of piezometers in a hillslope groundwater flow model in Modflow 6 and Model Muse. The tutorial covers all the steps related to the implementation of the observed points in Model Muse as well as the comparison among simulated and observed heads through scripts in Flopy.

June 15, 2021

A place to find MODFLOW executables for any operating system: Windows, Mac or Linux

June 15, 2021/ Saul Montoya

A normal distribution of the core versions of MODFLOW as well as its variants, and Modflow-Based particle tracking and solute transport models includes not only the executables for Windows, but also the documentation, source code, test problems and other utility programs. Working with the multiple tools of Modflow implies a huge collection of files that aren’t useful for the simulation itself if you are working on Windows. Modelers working on Mac or Linux had to compile our executable by themselves.

June 01, 2021

What we dont see in the development of open source software for groundwater modeling

June 01, 2021/ Saul Montoya

Usually we dedicate much time to developing tutorials and sometimes, just a few times, we actually write an article on this blog. Lately, our aim to discover and code is much greater than our impulse to give our opinion. This post is a special case where we write something without knowing if it is written because we are motivated or because there is something that needs to be written. In any case, writing this post doesn’t make us more free or happy... “Es macht uns nicht mehr zufrieden”... because we don´t know much about some things related to human nature.

February 01, 2021

Interactive MODFLOW MT3D transport model visualization with Flopy, Ipywidgets and Voila - Tutorial

February 01, 2021/ Saul Montoya

Representation and analysis of flow and transport results is a challenge for groundwater modelers. Aspects such as speed, compatibility, data format and visualization options are key in the 2D/3D representation of head and concentration on model cells. Under the Jupyterlab framework new tools have been developed that can be useful to represent model results on a user friendly way .

This time we have done a tutorial for the interactive representation of a contaminant plume in Jupyterlab; modeling was done with Modflow Nwt and Mt3d, representation was done with Matplolib, Ipywidgets and Voila.

January 18, 2021

Which are the challenges for model calibration in MODFLOW 6?

January 18, 2021/ Saul Montoya

MODFLOW 6 is the latest version of MODFLOW; we can’t frame this version as new because it has been released in May 2017 when QGIS 3 wasn’t even released or Python 3.6 was the latest version. On the hydrogeological perspective changes don't come as fast as expected and the amount of users of MODFLOW 6 is increasing but there are limitations on the pre/post processing tools that can take the best of the software for the general public.

Besides the philosophical discussion if a model can be “calibrated” or just “validated” there are some changes on the structure of MODFLOW 6 that bring challenges on the traditional way of model calibration.

January 06, 2021

Online Voronoi Modflow 6 groundwater modeling with Hakuchik - Tutorial

January 06, 2021/ Saul Montoya

Because a new year has come with a new way to model groundwater flow using the latest developments of Modflow 6 Disv. We are not exactly sure that we have done a tutorial, or a procedure or a bunch of code and tools together but we are sure that we have done something that can model geospatial groundwater flow online with awesome 3d representations. At the time we launched all the code on the Hakuchik server, we had a feeling of "we did it" and you are entitled to see if our work is good, bad or in progress. We are sure that more development needs to be done but this will be the way of groundwater modeling in the future, hoping that improving the capacities of professionals and concern of the general population will lead to a sustainable management of our groundwater resources.

December 23, 2020

Variable density groundwater flow modeling with MODFLOW 6 and BUY package - Tutorial

December 23, 2020/ Saul Montoya

Coastal aquifers and the interaction among brine / fresh groundwater need to be evaluated with a modeling code that can deal with variable density flow. For more than 18 years, SEAWAT was the prefered (or only) open source solution implemented in Modflow 2000 with some limitations* on its use with Flopy. Now in Modflow 6 the concept of simulation involves flow and transport modeling together with exchange among them. We have done a tutorial with a simple case of variable density flow from a saline lake into an acuifer. The transient model has a duration of 50 days where the saline water "intrudes" the aquifer at the bottom part of the lake.

November 16, 2020

Machine Learning Supported Groundwater Model Calibration with Modflow, Flopy, PySal and Scikit Learn - Tutorial

November 16, 2020/ Saul Montoya

We have done a tutorial on a low-level-complexity model with rivers, lakes, recharge and regional groundwater flow done in Model Muse in a previous tutorial. The model was imported as an object in Python with Flopy. A sensibility analysis was done with SALib to assess the response for the object model groundwater flow to a different sample of parameters and a resulting set of parameters and corresponding heads (parameters -> heads) were recorded. Then a machine learning regression was performed with Scikit-Learn with the inverse set (heads->parameters) to get the predicted parameters for the observed data. Different error measurements were performed for two model cases to assess the overall quality of the neural network regressor.

November 04, 2020

How to do a simulated groundwater head difference map in MODFLOW and ModelMuse - Tutorial

November 04, 2020/ Saul Montoya

This is a tutorial about some functionalities of Model Muse to analyze and process layer heads or parameters. The applied example was done based on a previous tutorial of a model with 3 stress periods, one static and two transient periods of 10 days. The simulated map shows the head difference in the last 10 days.

October 30, 2020

Review of the latest functionalities of the new release of MODFLOW 6 (mf6.2.0)

October 30, 2020/ Saul Montoya

Modflow6 is the latest version of the USGS code for groundwater modeling MODFLOW. This version has been coupled with another USGS open source software as Model Muse and Flopy and can implement diverse spatial discretization structures on a complete rearrangement of packages and keywords. We feel that there is a gap on the capabilities from a common groundwater modeler to adopt all the new development on Modflow and other open source groundwater software therefore we have prepared a video with the summary of this new release.

October 21, 2020

How to set a Multi Aquifer Well (MAW) in MODFLOW 6 and Model Muse - Tutorial

October 21, 2020/ Saul Montoya

Modeling the dynamic of the groundwater flow related to pumping was a challenge with the traditional Wel package in MODFLOW since wells are screened on the most part of the well depth crossing multiple layers of a groundwater flow model. The Multi Aquifer Well (MAW) package came as a solution for this complex behaviour of layer interaction in Modflow. Model Muse with Modflow6 can implement the MAW package with ease.

This tutorial shows the complete procedure to set up a MAW well on a 3 layer groundwater flow model, gives an overview of the package options and represents the well heads and well rates with scripts in Flopy.

August 30, 2020

Modeling impermeable walls with MODFLOW 6 and HFB Package - Tutorial

August 30, 2020/ Saul Montoya

Modeling the performance and effectiveness of flow barriers or impermeable walls on the groundwater flow regime is a challenge due to the wall geometry / orientation and discretization requirements. The package Horizontal Flow Barrier was designed to simulate barriers of defined thickness and conductances that are located in between flow cells, in this way the flow barrier is independent for the model discretization. This package is not new, it dates back to 1993, and it was implemented on many MODFLOW versions.

July 12, 2020

Tutorial of regional groundwater flow modeling with MODFLOW 6 and Model Muse 4

July 12, 2020/ Saul Montoya

Modeling groundwater flow on a regional scale has its own challenges because a regional model itself deals with refinement requirements, larger baselines, higher differences in elevations, complex geologies and areas without observation data.

The applied model of this tutorial covers the Angascancha Reservoir basin groundwater flow model in Ayacucho, Peru. This example have been modeled in several courses, tutorials and webinars with Modflow 2005, Flopy and Model Muse, however, this is the first time we port the model (succesfully) to Modflow 6 and Model Muse 4.

April 28, 2020

How to install Modflow 6 on Model Muse 4 - Tutorial

April 28, 2020/ Saul Montoya

Great free and open groundwater flow modeling software are in constant development process, therefore year by year we have newer versions or even new software. This time we have uptated a basic and useful tutorial from 2016 to the new version of Modflow and Model Muse. The tutorial shows the complete procedure to download and install Model Muse 4 and configure Modflow 6.

April 07, 2020

Tutorial of Regional Groundwater Modeling with Local Refinement using MODFLOW 6 - DISV and Model Muse 4

April 07, 2020/ Saul Montoya

We have explored the new (or not so new) options of Modflow 6 and Model Muse 4 to create local refinements on a regional scale based on hydraulic features. So far, we came up with a decent example of regional groundwater modeling on a andean basin with three boundary conditions and decreasing hydraulic conductivity with depth. The tutorial also explores the complexities to model basins with high difference on elevation and the use of text defined parameters to implement the Newton formulation in Modflow 6.

May 9, 2024

Diploma in Groundwater Modeling with Python and FloPy - Asynchronous

FloPy is the Python library that builds and executes MODFLOW models; this library has been enhanced to provide full support of MODFLOW 6 with most of its recent development is related to functionality for MODFLOW 6, tools to use vector and raster spatial data and common plotting and export functionality.

May 8, 2024

25% Off: Diploma in Applied Groundwater Modeling with MODFLOW and Model Muse - Asynchronous

We have designed a complete program on MODFLOW with Model Muse that ranges from the essential topics in flow and transport modeling to applied cases of regional modeling, infrastructure projects, and seawater intrusion. MODFLOW with Model Muse is a recent open-source software that provides various tools for simulating the groundwater flow regime in different environments.

30% Off: Program in Hydrological Modeling with SWAT+ and QGIS - Asynchronous

This program is designed to provide systematical learning from the most basic and general topics to intermediate and advanced topics, allowing the student to understand the various steps in developing hydrological models using the SWAT+ interface for QGIS. This program has a series of theoretical and practical concepts that allow the student to process spatial data, manage meteorological databases, build hydrological models, develop sensitivity analyses, and perform manual and automatic calibrations using versatile tools such as SWAT+ Toolbox, SQLite, and Python.

dataAnalysisOnlineTemperatureSensorThingAPIPython_en_12.png

October 1, 2026

Smart analysis of online temperature sensor data with SensorThingsAPI and Python - Tutorial

This tutorial demonstrates how to connect to a SensorThings API FROST server using Python to retrieve, inspect, and visualize IoT sensor datastreams. After setting up the server connection and querying datastream details such as units and observation counts, the notebook extracts time-series observations using paginated REST requests and loads them into a Pandas DataFrame. Following the data preparation phase, the script produces a series of continuous time-series line charts using Matplotlib and Seaborn, displaying the chronological trend of air temperature measurements recorded over time.

riverAquiferGeospatialGroundwaterModelmfVoronoiStudio_en_12.png

September 30, 2026

River Aquifer Groundwater Flow Model with mf6Voronoi Studio and Model Muse - Tutorial

This tutorial demonstrates how to build and simulate a groundwater model focused on river-aquifer interactions using open-source software. The workflow begins in mf6Voronoi Studio, where a Voronoi grid mesh is generated to capture complex spatial geometries efficiently. The mesh is then imported into ModelMuse, where key aquifer properties and essential boundary conditions—including general head, river, well, recharge, and evapotranspiration—are configured. After running the model, the simulated results are evaluated through an analysis of the water balance and head distribution.

September 29, 2026

Mesh Generation of Regional MODFLOW 6 Groundwater Flow Models with mf6Voronoi - Tutorial

In this tutorial we introduce mf6Voronoi, a specialized tool for generating optimized Voronoi meshes for regional groundwater models capable of spanning thousand of square kilometers. The video demonstrates how to set up and run a Python script using Anaconda Prompt, leveraging Dask parallel processing to refine mesh resolution along key rivers and riparian ecosystems while maintaining a coarse discretization elsewhere. By utilizing multi-core computing, the workflow reduces total mesh generation time by approximately 40–45%, delivering a high-resolution, multi-scale MODFLOW 6 mesh consisting of over 150,000 cells in just a few minutes.

September 28, 2026

Introduction to Online Sensor Analysis with SensorThings API and Python - Tutorial

In this Hatarilabs tutorial, viewers learn how to access and query live environmental sensor data using Python and the OGC SensorThings API standard. The video walks through setting up a Jupyter Notebook environment to interact with a FROST-Server, explaining key SensorThings API concepts—including Things, Sensors, Observed Properties, and DataStreams. Using packages such as requests, pandas, and datetime, the session demonstrates how to apply API parameters like $top, $skip, $orderby, and $expand to efficiently filter and retrieve time-series observations, culminating in a data frame visualization of temperature readings from a live outdoor sensor.

September 22, 2026

Regional groundwater flow modeling with mf6Voronoi Studio and Model Muse - Tutorial

In this tutorial, we demonstrate how to build a regional groundwater flow model of an Andean basin using MF6Voronoi Studio and ModelMuse.

Generating flexible, non-rectangular meshes has historically been one of the most challenging steps in Modflow 6 modeling. MF6Voronoi Studio addresses this by providing a graphical interface for Python-based Voronoi mesh generation (DISV), allowing high-resolution cell refinement along river networks while maintaining a coarse mesh across the broader basin.

Blog