The HYDRUS-1D and HYDRUS (2D/3D) computer software packages are widely used finite-element models for simulating the one- and two- or three-dimensional movement of water, heat, and multiple solutes in variably saturated media, respectively. In 2008, Šimůnek et al. (2008b) described the entire history of the development of the various HYDRUS programs and related models and tools such as STANMOD, RETC, ROSETTA, UNSODA, UNSATCHEM, HP1, and others. The objective of this manuscript is to review selected capabilities of HYDRUS that have been implemented since 2008. Our review is not limited to listing additional processes that were implemented in the standard computational modules, but also describes many new standard and nonstandard specialized add-on modules that significantly expanded the capabilities of the two software packages. We also review additional capabilities that have been incorporated into the graphical user interface (GUI) that supports the use of HYDRUS (2D/3D). Another objective of this manuscript is to review selected applications of the HYDRUS models such as evaluation of various irrigation schemes, evaluation of the effects of plant water uptake on groundwater recharge, assessing the transport of particle-like substances in the subsurface, and using the models in conjunction with various geophysical methods.

The capabilities of the HYDRUS-1D and HYDRUS (2D/3D) software packages continuously expanded during the last two decades. Various new capabilities were added recently to both software packages, mostly by developing new standard add-on modules such as HPx, C-Ride, UnsatChem, Wetland, Fumigant, DualPerm, and Slope Stability. The new modules may be used to simulate flow and transport processes in one- and two-dimensional transport domains and are fully supported by the HYDRUS graphical user interface (GUI). Several nonstandard add-on modules, such as Overland, Isotope, and Centrifuge, have also been developed, but are not fully supported by the HYDRUS GUI. The objective of this manuscript is to describe several additional features of the upcoming Version 3 of HYDRUS (2D/3D), which was unveiled at a recent (March 2017) HYDRUS conference and workshop in Prague. The new features include a flexible reservoir boundary condition, expanded root growth features, and new graphical capabilities of the GUI. Mathematical descriptions of the new features are provided, as well as two examples illustrating applications of the reservoir boundary condition.

A broad range of numerical models have been developed during the past several decades to describe the fate and transport of agricultural, industrial, and other contaminants in soils and groundwater. Such models are now increasingly implemented in both research and engineering projects addressing subsurface pollution problems. Of particular concern is especially non-point source pollution stemming from plant and animal production. In this paper we first briefly review different types of mathematical models that are being used to describe the transport of agricultural chemicals in both the vadose zone and groundwater. We next review various versions of the HYDRUS computer software packages, including several specialized modules that were recently developed for simulating the movement of water, heat, and solutes in the subsurface. Early versions of the HYDRUS models considered the transport of only one chemical species and assumed that the behavior of this solute was independent of other species present in the soil solution. Physical non-equilibrium transport could be accounted for in later versions of HYDRUS by assuming a two-region or dual-porosity type formulations that partition the liquid phase into mobile and immobile regions. Chemical non-equilibrium transport could be accounted for by assuming kinetic interactions between solutes in the liquid and solid phases. Physical and chemical non-equilibrium formulations were extended later also to particle transport by including provisions for filtration theory, and time- and/or depth-dependent blocking functions. Subsequent versions of the HYDRUS codes also considered the transport of multiple solutes, which either could be coupled by means of a unidirectional first-order degradation chain, or move independently of each other. While this approach proved effective for evaluating the subsurface transport of many chemicals (e.g., nitrogen species, pesticides, radionuclides), many environmental problems require analyses of the transport of multiple chemical species that could interact mutually, create complexed species, precipitate, dissolve, and/or compete with each other for sorption sites. Several specialized modules have now been developed to simulate transport processes not accounted for in the earlier standard versions of HYDRUS. These include a wetlands module, the HP1/2/3 multicomponent transport modules, the facilitated transport C-Ride module, a module for fumigants, and the major ion Unsatchem module. All of these modules simulate flow and transport processes in two-dimensional transport domains and are supported by the HYDRUS (2D/3D) graphical user interface. Many processes of these specialized modules are also available as part of the public domain HYDRUS-1D software. Brief overviews of these more recent modules are included in this manuscript. © Indian Institute of Science.