The importance of hydrogen bonds and solvent effects in soil and environmental chemistry is demonstrated in this chapter. Humic substances as one of the major soil constituents are modeled by means of representative functional groups. Their capability to form hydrogen bonds is demonstrated on interactions with selected sets of polar molecules, anions and acidic pesticides, particularly 2,4-dichlorophenoxyacetic. It was shown that anionic species form complexes of similar strength as corresponding neutral molecules if solvent effects are taken into account. Of all functional groups carboxyl showed the highest chemical activity in the formation of complexes. The calculations demonstrate that the solvent effect substantially lowers the complex formation energies, especially in case of charged systems. The soil minerals kaolinite and goethite studied in this work possess very active surfaces, which are formed from hydroxyl groups. These OH groups are very flexible and able to act as a proton donor or acceptor for hydrogen bond formation. Polar molecules (e.g., H2O, acetic acid) form strongly bound complexes via multiple hydrogen bonds. It was shown that strong sorbent sites exist on irregular clay mineral surfaces formed on the corner and edges of clay mineral particles.