Future agriculture calls for increased input (e.g., water, nutrients, pesticides) use efficiency while maintaining or improving productivity, minimizing environmental impacts, and increasing profitability. Complete understanding of complex irrigation systems requires laborious, time-consuming, and expensive field investigations, which invariably involve only a limited number of treatments. On the other hand, fully calibrated process-based models, such as HYDRUS, can quickly evaluate different irrigation management strategies without the need for labor-intensive fieldwork and have become valuable research tools for predicting complex and interactive water flow and solute transport processes in and below the root zone. HYDRUS codes have been used worldwide in several hundreds of studies evaluating various types of irrigation (e.g., sprinkler, furrow, basin, and surface and subsurface drip), their scheduling (e.g., the timing of irrigation and its amount), and solute-related factors (e.g., fertigation, chemigation, salinization, and sodification). The objective of this manuscript is to review the current modeling capabilities of HYDRUS to evaluate various irrigation methods and related processes. The manuscript starts with a section describing governing flow and transport equations solved numerically by the HYDRUS codes, the corresponding initial and boundary conditions, and related factors such as soil hydraulic properties and root water and nutrient uptake. Modeling of different irrigation techniques is described in subsequent sections, followed by sections dealing with solute-related topics such as fertigation, chemigation, and salinization/sodification. Topics, including the effects of spatial variability, optimization of irrigation systems, and special irrigation methods, are covered in the later sections. The manuscript emphasizes the advantages and opportunities of HYDRUS in describing various processes in the root zone of irrigated plants that support sustainable irrigated agriculture. All the project files of the discussed examples and their descriptions are available for download at https://www.pc-progress.com/en/Default.aspx?hyd5-AdvancesInAgronomy.