Mathematical models have become indispensable tools for studying vadose zone flow and transport processes. We reviewed the history of development, the main processes involved, and selected applications of HYDRUS and related models and software packages developed collaboratively by several groups in the United States, the Czech Republic, Israel, Belgium, and the Netherlands. Our main focus was on modeling tools developed jointly by the U.S. Salinity Laboratory of the USDA, Agricultural Research Service, and the University of California, Riverside. This collaboration during the past three decades has resulted in the development of a large number of numerical [e.g., SWMS_2D, HYDRUS-1D, HYDRUS-2D, HYDRUS (2D/3D), and HP1] as well as analytical (e.g., CXTFIT and STANMOD) computer tools for analyzing water flow and solute transport processes in soils and groundwater. The research also produced additional programs and databases (e.g., RETC, Rosetta, and UNSODA) for quantifying unsaturated soil hydraulic properties. All of the modeling tools, with the exception of HYDRUS-2D and HYDRUS (2D/3D), are in the public domain and can be downloaded freely from several websites.