HYDRUS is based on finite element method which allows designing complicated mesh grids in triangular geometry, but Visual MODFLOW is based on finite difference technique and barely finite volume (e.g., TVD scheme) which allows designing only rectangular mesh grids. HYDRUS can simulate both saturated and unsaturated conditions with its core scheme, but the main models in Visual MODFLOW (MODLFW, MT3DMS, SEAWAT) are unable to simulate the unsaturated flow condition, although SEAWAT can simulate the variable density flow, e.g., saline water. HYDRUS can also consider the vadose zone, uptake of plant, infiltration and so forth. Visual MODFLOW links the groundwater transport models with surface water, e.g., through Mike 11. HYDRUS can optimize the parameters by its built-in Marquardt-Levenberg algorithm. Visual MODFLOW uses the WinPEST which can optimize the parameter with the same algorithm, but  by 2012 it was not possible to optimize most of the solute transport parameters by the software directly and you had to build the input files of WinPEST by yourself. HYDRUS has a demo version in public domain but Visual MODFLOW is free in full version only for one month. The most magnificent point about HYDRUS is that recently it has been applied and modified to simulate the colloid and nanoparticle transport in porous media with considering various phenomena of attachment, detachment, blocking, ripening, and straining. We recently modified MODFLOW too to simulate the transport of nanoparticles with considering the aggregation phenomena. 

Hope this helps

I do not have experience with Hydrus. But worked a little with Modflow. I found visual modflow interface friendly. The post processor was good enough. However, I would suggest to chose based on your problem. for example, i would difinitely go for Modflow flex for salinity intrusion ( my choice).

As S H Bari I do not have experience with Hydrus.  For solute transport I used MT3DMS coupled with Modflow and for reactive transport RT3D. PMWIN is a very friendly and easy modeling environment that calls all those models.

Dear Muhammad,

With Visual MODFLOW Flex, you have a complete set of tools that allow you to treat the water quality, groundwater flows, and initiatives concerning the protection of spring water, thanks to:

- SEAWAT v.4 - groundwater flow with variable density in 3D, associated with solute transport for several species and heat transfer

- MT3DMS - Package Standard simulation of pollutant transport for several species

- MODPATH - Standard Package modeling the particle path.

 Why is it recommended to use Visual MODFLOW Flex?

- Build models faster and more effectively

- Build larger and more complex models

- Improve your Reliability Models for Groundwater Flow

- Delete Third International Aid & Debt Costs with Integrated Modeling

With my best regards

Prof. Bachir ACHOUR

HYDRUS is based on finite element method which allows designing complicated mesh grids in triangular geometry, but Visual MODFLOW is based on finite difference technique and barely finite volume (e.g., TVD scheme) which allows designing only rectangular mesh grids. HYDRUS can simulate both saturated and unsaturated conditions with its core scheme, but the main models in Visual MODFLOW (MODLFW, MT3DMS, SEAWAT) are unable to simulate the unsaturated flow condition, although SEAWAT can simulate the variable density flow, e.g., saline water. HYDRUS can also consider the vadose zone, uptake of plant, infiltration and so forth. Visual MODFLOW links the groundwater transport models with surface water, e.g., through Mike 11. HYDRUS can optimize the parameters by its built-in Marquardt-Levenberg algorithm. Visual MODFLOW uses the WinPEST which can optimize the parameter with the same algorithm, but  by 2012 it was not possible to optimize most of the solute transport parameters by the software directly and you had to build the input files of WinPEST by yourself. HYDRUS has a demo version in public domain but Visual MODFLOW is free in full version only for one month. The most magnificent point about HYDRUS is that recently it has been applied and modified to simulate the colloid and nanoparticle transport in porous media with considering various phenomena of attachment, detachment, blocking, ripening, and straining. We recently modified MODFLOW too to simulate the transport of nanoparticles with considering the aggregation phenomena. 

Hope this helps