**1. Introduction**

In the past few decades, more attention is devoted to environmental protection and pollution control in the soil‐plant‐atmosphere continuum. There are growing numbers of potentially harmful substances that are introduced in the environment, especially by agricultural practi‐ ces and industry in arable and urban areas. Such substances can accumulate in the soil (and potentially get into food chain), surface water, or can be transported in a deeper soil zone and eventually reach groundwater. Intensive agriculture uses large amounts of fertilizer (organic and inorganic), plant protection products (pesticides), animal hormones, and include various other substances that may accumulate in environment (e.g. pathogens, bacteria, and trace metals). Although most of the substances applied in agricultural production are useful in the surface layer of the soil, due to their leaching into the deeper soil layers and groundwater and their bioaccumulation potential, they can also cause serious pollution and degrade natural resources.

Water flow and solute (pollutant) transport models can be used as tools for describing and predicting specific processes in variably saturated soil zone or vadose zone. For example, different models can be used for predicting and/or management of irrigation and drainage systems, crop growth, fertilizer application, and pesticide leaching to protect soil and water resources. Models are also equally necessary for the design of waste disposal sites (industrial, municipal) or long‐term management of various harmful substances (e.g. radioactive waste). A large number of models were developed to simulate the numerous simple hydraulic or complex biogeochemical processes and may be used for different purposes. Vadose zone is in focus of many research topics due to its complex nature and also the possibility of elimination and remediation of present/introduced contaminants before leaching to underground water resources.

Transfer of solutes in the soil is closely linked with the flow of water through vadose zone, which largely affects the concentration and biochemical reactions of various substances. Solute transport in soil vadose zone is one of the most demanding problems that occur in numerical modelling. It includes the transport of water and solutes, chemical reactions and microbial transformations. With the development of new numerical models, it is possible to describe more complex processes that are occurring in the soil‐plant‐atmosphere continuum. In this chapter, basic soil physical concepts and numerical modelling procedures (with example) are explained. Trace metal behaviour in the ecosystems, their mobility in soil, and metal chemical forms (species) in the soil solution are shortly discussed with a chemical speciation modelling example presented.
