Soil minerals represent chemically important and active inorganic components of soils playing a considerable role in many physical chemical processes in soils. Soil processes are very complex and, although intensively investigated experimentally, are not always fully understood. Intermolecular interactions are often dominant forces in these processes and have a substantial effect on the fate of chemical species in soil matrices. Thus, it is extremely useful to describe these interactions at a detailed molecular level, which can be a key to understand underlying mechanisms of processes going on in soil interfaces. During the last decade applications of computer simulation methods in material chemistry rapidly increased. It seems that these methods based on molecular modeling approaches can also be an important tool for experimentalists in soil science. Nowadays a broad range of simulation methods exists - from conventional molecular mechanics based on empirical potentials to exact ab initio approaches. The former ones are cheap and fast and at the present state of computational facilities able to treat thousands of molecules in a time scale of µ-seconds. However, their reliability is often limited due to the accuracy of empirical interatomic potentials. On the other hand, ab initio methods are more accurate and reliable but also more time consuming than the previous ones what means that they are mainly limited in size and time scales. Simulations (relaxation and/or molecular dynamics) of surfaces of soil minerals (namely kaolinite, montmorillonite and goethite) and interactions between these minerals and several molecules (water, acetic acid, phenoxyacetic-acid derivatives and benzene). These interactions are studied using models with isolated molecules on surfaces and in some cases using models in which solvent effects are considered by including water molecules explicitly in the simulation. The role of cations present in the soil solution on the formation of the surface complexes is investigated too. Structural, energetic and dynamic properties are evaluated from the simulations and possible sorption mechanisms are discussed.