J. Hydrol. Hydromech., 66, 2018, 2, 129–132
DOI: 10.1515/johh-2017-0060

Thematic Issue on HYDRUS Software Applications to Subsurface Fluid Flow
and Contaminant TransportJiří Šimůnek1*, Martinus Th. van Genuchten2, 3, Radka Kodešová4
1

Department of Environmental Sciences, University of California, Riverside, CA, USA.
Center for Environmental Studies, CEA, São Paulo State University, UNESP, Rio Claro, SP, Brazil.
3
Department of Earth Sciences, Utrecht University, Netherlands.
4
Department of Soil Science and Soil Protection, Czech University of Life Sciences, Prague, Czech Republic.
*
Corresponding author. E-mail: Jiri.Simunek@ucr.edu
2

INTRODUCTIONHYDRUS DEVELOPMENT AND APPLICATIONSThis thematic issue documents selected presentations given
at the Fifth International Conference on “HYDRUS Software
Applications to Subsurface Flow and Contaminant Transport
Problems,” held in Prague, Czech Republic, March 30–31,
2017, as well as several other papers by authors who did notattend the conference. Previous conferences in the HYDRUS
series were held in Utrecht in 2005, in Tokyo in 2008, and in
Prague in 2008 and 2013. The conferences focused on the development and application of advanced numerical models simulating fluid flow, heat transport, and/or the transport of various
contaminants or other solutes (such as nutrients, pesticides,
heavy metals, radionuclides, and pathogenic microorganisms)
in variably-saturated soils and groundwater. The conferenceswere designed to bring together users of the HYDRUS familyof codes, as well as of related software, to review and exchange
information on various aspects of the codes, future enhancements of the software, and their application to a broad range ofsoil, environmental, hydrological, ecological, and agriculturalproblems.
Since the first conference in 2005, the community of HYDRUS users has been growing continuously as evidenced by
the number of downloads (over 10,000 times each of the past
several years) and visits to the HYDRUS web pages (several
hundred on average each day). Hundreds of journal articles
have been published in which the HYDRUS codes have beenused (see the review by Šimůnek et al., 2016). Feedback fromusers such as those attending the HYDRUS conferences has
been extremely important in terms of identifying particularstrengths and weaknesses of the codes, defining additional
processes or features that should be included in the models, or
identifying key challenges and new perspectives in modeling a
multitude of interacting soil physical, chemical, and biologicalprocesses (Vereecken et al., 2016).
Although the HYDRUS codes are now widely used formodeling biogeochemical processes in the vadose zone, a large
number of alternative subsurface flow and transport models canbe used for similar applications. Popular existing codes (such as
MODFLOW-SURFACT, STOMP, SWAP, VS2DI, andTOUGH2) are discussed in detail in a special 2008 issue“Vadose Zone Modeling” of Vadose Zone Journal (Šimůnek
and Bradford, 2008), while a more extensive inventory ofavailable models is provided in the Encyclopedia of
Hydrological Sciences (Šimůnek, 2005). Steefel et al. (2015)
further provided a review of more comprehensive reactive
transport codes for subsurface environmental simulations. We
refer readers to these additional resources for more information
about alternative subsurface flow and transport models.

This special issue contains 12 contributions from HYDRUS
software users, covering a range of topics from the very fundamental to important practical applications. The leading paper byŠimůnek et al. (this issue) describes new features that will beavailable in Version 3 of the HYDRUS (2D/3D) computer
software package. Several important new features have been
implemented recently in the standard computational module ofVersion 3. The most important additions relate to root growth
and the use of a reservoir boundary condition. While HYDRUS-1D allowed users to prescribe a time-variable rooting
depth, using either the logistic growth function or some tabulated form upon input, HYDRUS (2D/3D) thus far assumed thatthe spatial distribution of roots in the root zone remained constant during the simulations. Šimůnek et al. (this issue) discuss
multiple adaptations to overcome this shortcoming. Also,
earlier versions of HYDRUS (2D/3D) required pressure heads
at boundaries representing external water bodies, such as
pumping wells or agricultural furrows, to be specified as anexternal input, without any feedback that would relate possible
changes in their water level in response to flow processes
within the subsurface (such as infiltration or exfiltration). The
upcoming new HYDRUS version has now an option to accountfor such interactions using a new reservoir boundary condition.
The new root growth and reservoir boundary features wererequested by many HYDRUS users; they should undoubtedly
extend the applicability of the code to a much broader range ofapplications. Additionally, the GUI of HYDRUS (2D/3D) has
been completely rewritten to ensure compatibility with new
Windows operating systems and the development of more
efficient software in the near future (Šimůnek et al., this issue).
Multiple new tools, such as Manipulator, Clipper, and Slicer, as
well as the use of 3D streamlines, were developed for Version 3of HYDRUS (2D/3D) and are discussed briefly by the authors.
The remaining papers in the thematic issue can be divided
into two groups. The first group of papers uses existing standard HYDRUS modules and describes their application to a wide
range of problems. Applications range from evaluations of a)the effects of temporal averaging of meteorological data on
predictions of groundwater recharge (Batalha et al., this issue),b) flow in capillary barriers (Berger, this issue), c) the Hyprop
evaporation method for estimating the unsaturated soil
hydraulic properties (Bezerra Coelho et al., this issue), d) the
effects of soil water repellency on the unsaturated soil hydraulicproperties (Filipović et al., this issue), e) the impact of stones in
actual field soils of the High Tatras mountains in Slovakia on
soil water storage and recharge (Hlaváčiková et al., this issue),f) how changes in cropping patterns at a large scale can produce129Jiří Šimůnek, Martinus Th. van Genuchten, Radka Kodešováwater savings and social gains (Karimov et al., this issue), to g)
137
Cs transport from the Goiânia Radioactive Waste Repository
in Brazil towards groundwater (Pontedeiro et al., this issue).
These applications quite nicely demonstrate the breadth ofpossible applications of the HYDRUS software packages.
The second group of papers focuses either on applications ofexisting special add-on modules of HYDRUS, such as HPx for
multicomponent contaminant transport (Jacques et al., thisissue) and the Wetland module (Pucher and Langergraber, thisissue), or on coupling the HYDRUS code with DSSAT (Shelia
et al., this issue) or the SWI2 package of MODFLOW(Szymkiewicz et al., this issue). DSSAT is a suite of field‐scale,process‐based crop models that simulate the phenological development of crops to obtain detailed information about various
yield components from emergence till maturity on the basis ofcrop genetic properties, environmental conditions (soil, weather) and management options (Jones et al., 2003). MODFLOW
is the U.S. Geological Survey (USGS) modular finitedifference flow model (McDonald and Harbaugh, 2003), whichis considered to be the de facto standard code for simulating
groundwater flow. The SWI2 package for MODFLOW may be
used to represent in a simplified way variable-density flow
associated with saltwater intrusion in coastal aquifers (Bakker
et al., 2013).
Applications of the standard HYDRUS modules
The first paper of this first group of papers discusses the effects of temporal averaging of meteorological data on predictions of groundwater recharge. Batalha et al. (this issue) used
HYDRUS-1D to show that temporal averaging of meteorological data can lead to significant bias in predictions of groundwater recharge. They found that an increase in the duration of theaveraging interval of meteorological data (from hourly, daily,
weekly, monthly to yearly time periods) will lead to lower
estimates of groundwater recharge, especially at sites havingcoarse-textured soils. At one of the study sites in Brazil, daily
averaged data produced recharge rates almost ten times greaterthan those obtained using yearly averaged data (Batalha et al.,this issue). This same problem was also studied, with similar
conclusions, by Szymkiewicz et al. (this issue) using the HYDRUS package for MODFLOW.
Berger (this issue) used the two-dimensional version of
HYDRUS (2D/3D) to evaluate experimental data collected at a
10-m tipping trough representing capillary barriers. Capillarybarriers are two-layered systems consisting of an upper layer
made up of relatively fine-grained porous material (the capillary layer) underlain by a lower layer consisting of relatively
coarse-grained porous material (the capillary block). Water
percolating through the capillary layer under unsaturated conditions is then held above the interface between the two layers
due to capillary forces and the large difference in their soil
hydraulic conductivities. While HYDRUS described flow
through the capillary layer and the capillary block relatively
well, the software failed to reproduce an abrupt change in theflow pattern that was observed experimentally when increasing
rainfall. Instead, the model produced a relatively smooth pattern
without any distinct thresholds. Berger (this issue) discusses indetail possible causes for this mismatch, including experimental
issues, the application of the model, or the model itself.
An application of HYDRUS-1D to the HYPROP evaporation method for estimating the unsaturated soil hydraulic properties is discussed by Bezerra Coelho et al. (this issue). Whileearlier applications of HYDRUS-1D using the evaporation
method appeared many years ago (e.g., Schelle et al., 2010;

130

Schindler et al., 2010; Šimůnek et al., 1998), Bezerra Coelho etal. (this issue) provide a much more complete analysis of themethod. They used HYDRUS-1D to carry out an independent
analysis of the HYPROP system, which standardized the evaporation method, for a broad range of soil textures. The authors
conclude that overall, the HYPROP methodology performed
extremely well for most soil textures and as such constitutes amuch-needed addition to current soil hydraulic measurement
techniques (Bezerra Coelho et al., this issue).
An important factor affecting the hydraulic behavior ofmany soils that is projected to increase in importance due toglobal climate change is soil water repellency. This feature israrely modeled successfully using numerical models based on
the standard Richards equation (e.g., Deurer and Bachmann,
2007; Diamantopoulos et al., 2013; Robinson et al., 2010).
Filipović et al. (this issue) use HYDRUS (2D/3D) to estimate
the hydraulic properties of soils exhibiting water repellency
using experimental data collected with a disc infiltrometer, andwith water and ethanol as the infiltration liquid. They then usedthe calibrated model to assess the water balance of a hillslope
containing soils exhibiting different degrees of water repellency.
Another important factor that affects subsurface water flow,
especially in mountainous areas, is the presence of stones that
could dramatically constrain the soil volume through whichwater moves. While stony soils have been studied in the pastusing HYDRUS (2D/3D) (e.g., Hlaváčiková et al., 2016; Novák
et al., 2011; Parajuli et al., 2017), those studies considered only
hypothetical soil systems with simplified geometries and idealized distributions of stones. Hlaváčiková et al. (this issue) inthis issue used HYDRUS-1D to assess the impact of stones inreal soils of the High Tatras mountains in Slovakia on soil
water storage and recharge. Their studies indicate that the presence of rock fragments in a moderate-to-high stony soil cansignificantly decrease the soil water storage (by some 25% ormore) and affect the soil water dynamics.
Karimov et al. (this issue) used HYDRUS-1D to assess howchanges in the large-scale cropping patterns of the Fergana
Valley in Central Asia can produce water savings and social
gains. They examined possible water savings by replacing
alfalfa with winter wheat (with either a fallow period or thecultivation of green gram during the summer) for various
irrigation scenarios such as high-deficit versus low-deficit
irrigation. Karimov et al. (this issue) discussed not only varioushydrological components (e.g., transpiration, evaporation, andrecharge), but also the many economic and social gains that
could be obtained with different cropping scenarios within arelatively broad developmental context.
Finally, Pontedeiro et al. (this issue) used HYDRUS-1D toreassess the Goiânia Radioactive Waste Repository in Brazil
stemming from an accident in 1987 with an abandoned cesium
chloride teletherapy source. They first obtained estimates ofwater infiltrating through the soil cover on top of the repository
into and through the waste and its concrete liners and the underlying vadose zone towards groundwater. Interestingly, calculations accounted not only for hydrological fluxes resulting fromlocal precipitation and evapotranspiration, including root water
uptake by the grass cover, but also for the effects of concretedegradation on the hydraulic properties of the liners. Next,
137
Cs transport from the repository towards groundwater wasconsidered while accounting for the effects of 137Cs sorption
and radioactive decay. Results indicated that very little if any
radioactive material would reach the water table during theapproximately 400-year lifespan of the repository, even when
accounting for preferential flow through the waste using a dualporosity (mobile-immobile water) contaminant transport model.

Thematic Issue on HYDRUS Software Applications to Subsurface Fluid Flow and Contaminant Transport

Development and applications of HYDRUS add-on modules
A large number of standard and non-standard add-on modules have been developed over the years to expand the applicability of the HYDRUS software packages. As summarized byŠimůnek et al. (2016) these modules include, but are not limited
to, a) the UnsatChem module that simulates the transport andreactions of major ions, b) the HPx modules that consider
various general biogeochemical reactions in soils, c) the C-Ride
module that simulates the colloid-facilitated solute transport, d)
the Wetland module that considers various biogeochemical
reactions in constructed wetlands, e) the DualPerm module forsimulations of nonequilibrium and/or preferential flow andtransport, f) the Fumigant module that considers the fate andtransport of fumigants, and g) the Isotope module to simulate
the fate and transport of isotopes. The current thematic issue
contains two manuscripts describing applications of two ofthese modules, notably the HPx module (Jacques et al. thisissue) and the Wetland module (Pucher and Langergraber, thisissue). Additionally, two manuscripts describe the coupling of
HYDRUS-1D with DSSAT (Shelia et al., this issue) and
MODFLOW (Szymkiewicz et al., this issue).
Jacques et al. (this issue) describe recent developments andapplications of the HPx modules for multicomponent reactive
transport during variably-saturated flow. The HPx modules area result of coupling the HYDRUS computational codes with
PHREEQC (Parkhurst and Appelo, 2013). They may be used tosimulate one- and multi-dimensional water flow and solutetransport, in conjunction with a large number of biogeochemical reactions, in variably-saturated soils and other porous systems. Jacques et al. (this issue) gave an overview of the mostsignificant recent developments of HPx, such as the coupling of
hydraulic properties with geochemical state variables (e.g.,porosity and hydraulic conductivity), considering gaseous diffusion, and facilitating transport in two and three dimensions.
They provide multiple examples demonstrating the use of HPx
to simulate a range of processes relevant to soil organic matter
dynamics in soils, the fate of dissolved organic matter and CO2transport in soils, as well as bioturbation processes.
Pucher and Langergraber (this issue) analyzed four verticalflow wetland systems using the Wetland module of HYDRUS(2D/3D). The Wetland module (Langergraber and Šimůnek,2012) was developed in order to simulate governing biologicaland chemical transformation and degradation processes ofwastewater constituents in subsurface flow treatment wetlands.
Pucher and Langergraber (this issue) evaluated whether thedefault values of various biological and chemical parametersprovided by the Wetland module can be used to represent collected experimental data. Their results indicate that for verticalflow wetlands with fine sand, no adjustments of the standard
parameter set were needed, while for systems with coarser filter
media as the main layer, the standard parameter set had to be
adjusted to match simulated and measured effluent concentrations.
The HYDRUS codes previously have been coupled withseveral crop and/or root growth models as reviewed byŠimůnek et al. (this issue) and Hartmann et al. (2018). Shelia etal. (this issue) report another recent development, i.e., the implementation of HYDRUS flow routines into the DSSAT cropmodeling system. DSSAT refers to a suite of field‐scale, process‐based crop models that simulate the phenological development of crops, including detailed information about various
yield components, from emergence till maturity on the basis ofcrop genetic properties, environmental conditions (soil, weather) and management options (Jones et al., 2003). While the

DSSAT system thus far relied on the “tipping bucket” waterbalance approach to represent soil hydrologic and water redistribution processes, implementation of the HYDRUS flowroutines into DSSAT allows one to use now the more processbased Richards equation to represent these processes. The advantages and disadvantages of the two approaches are wellknown and have been discussed elsewhere (e.g., Scanlon et al.,2002). Shelia et al. (this issue) provide details about the coupling of the two models, as well as applications of the two
approaches to multiple datasets involving not only measured
water contents, but also multiple crop growth variables.
The last paper of this thematic issue (Szymkiewicz et al.,this issue) discusses the simultaneous use of the HYDRUS and
SWI2 packages for MODFLOW to simulate freshwater lensrecharge and the position of the salt/freshwater interface. The
study was applied to a sandy peninsula, a typical geomorphologic setting in many coastal areas such as along the Baltic andNorth Sea coasts. The MODFLOW groundwater flow model
comes with a large number of "packages" to account for various
processes, such as recharge from the vadose zone, and interactions with rivers and ponds. The HYDRUS package for MODFLOW is one such package that considers processes in thevadose zone (Beegum et al., 2018; Twarakavi et al., 2008). The
SWI2 package is another package, which may be used to represent in a simplified way variable-density flow associated withsaltwater intrusion in coastal aquifers (Bakker et al., 2013).
Szymkiewicz et al. (this issue) used both packages simultaneously to highlight the sensitivity of calculated recharge rates tothe temporal resolution of weather data (similarly as Batalha etal., this issue), leading to different trends in the evolution of
freshwater-saltwater interfaces. They also found that root water
uptake can significantly influence both the recharge rate and theposition of the freshwater-saltwater interface.
CONCLUSIONSThe twelve papers in this thematic issue reflect the considerable depth and breadth of possible applications of the HYDRUS software packages and their specialized add-on modules.
The thematic issue also indicates continuous improvement of
the codes themselves and their GUI’s, including thedevelopment of new features such as more flexible root growth
options and a dynamic reservoir boundary condition, as well as
coupling of the HYDRUS codes with separate crop growthmodels (e.g., DSSAT), biogeochemical models (e.g.,
PHREEQC), or larger-scale flow and transport models (e.g.,
MODFLOW). These improvements keep enhancing in minor
and major ways the applicability of the HYDRUS family ofcodes to existing or new applications, and to new areas of research. They provide important additions to the many standard
and non-standard add-on HYDRUS modules discussed in detailby Šimůnek et al. (2016).
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