A new and fresh opensource preprocessing and post processing tool is available. Freewat 0.4 was launched as a beta version and publicly available upon registration from this website: http://freewat.eu/. Most of the developers are italian and the project is funded under the H2020 program from the European Union and the Regione Toscana. The software comes with clear and descriptive documentation and tutorials plus the installation instructions.
This article show the most important features of Freewat and its capabilities for representing the geospatially referenced regional groundwater flow.

Why is it important to have a georeferenced groundwater flow?

MODFLOW itself do not care about spatially referenced groundwater flow, it does calculate water heads and flow in between cells. It didn't matter matter where the model was, it could be in Peru, Alaska, Germany or Nepal. Actually the only geoference for a Modflow build with Model Muse was some comment on the discretization file (.DIS file) useful only by a pre/post processing tool.
Under the open source stack, if you wanted to plot the results of your groundwater flow model as heads, water table, or drawdown on a GIS software you had to manually export MODFLOW output as shapefiles and import it on QGIS for example.
An medium/advance groundwater modeler can work 50% on GIS and 50% on MODFDLOW, an advance user could even automatize the map generation of MODFLOW results by scripts on PyQGIS and Flopy. But lets focus on a beginner user, lets try to create a user friendly interface, and most importantly, lets create and develop attention on the impact assessment on the groundwater flow. If you provide a tool where you can use your own GIS data, and develop a MODFLOW model on the same tool, that would create a nice scientific "atmosphere" for the user and the discussion of results.
Groundwater flow modeling with tools as MODFLOW is not a easy tool, because it has to deal with complexities as understanding an heterogeneous and anisotropic nature plus dealing with numerical requirements, residual non-convergences, observed-calculated calibration criteria. That is one reason why we have less groundwater flow modelers than surface flow modelers, and we require more.
If we provide a simple tool as Freewat based on a simple GIS software as QGIS, we could enhance the learning curve of beginner MODFLOW modelers for two main reasons:

Because they don't have to change of software
Because the input and output are GIS layers

Later on, these users can shift if required to other tools or even they can run their model on pure MODFLOW.

What is new on Freewat?

Freewat is new and comes with the some of the latest development of MODFLOW as Flopy, OWHM, MT3D, UCODE, UZF and others. If you are not a regular Python user, you might not be aware of the Flopy library. Flopy was developed as a tool for MODFLOW model construction and simulation based on Python scripts. With Freewat it is possible to use Flopy tools on QGIS without the programming skills, although we recommend to learn some Python if you want to be a modeler.
With the following tools implemented in Freewat you can perform the following tasks:

MODFLOW 2005:

Numerical simulation of 3d groundwater flow on steady and transient conditions considering boundary conditions as rivers, drains, wells, recharge, evapotranspiration, lakes and reservoirs. Freewat implement unsaturated flow on the vadose zone and surface water routing.

MT3D:

Solute transport modeling useful for assessment of contaminant plumes on the groundwater flow. This package is a USGS latest version of MT3DMS and allows the representation of sources and sinks of contaminants, advection and dispersion process and it can represent chemical reactions (speciation/precipitation/decay) of contaminants.

MODFLOW OWHM:

A integrated hydrological flow model designed for the analysis of cases of conjunctive use of groundwater and surface water. This code allows the simulation, analysis and management of human and natural flow with a physical framework of supply and demand.

UCODE:

A useful tool for the sensibility analysis and automatic parametrization. However, a responsible hydrogeologist uses the automatic parametrization as a tool that can give you some hints of the actual hydraulic parameters values, and not as a tool that perform the whole calibration itself. Remember, the computer does not know hydrogeology (yet).