This chapter is concerned with the role of micro-organisms in soils in respect to the degradation and transformation of organic contaminants in particular, and certain applicable inorganic contaminants. The various types of common micro-organisms found in typical soils are first presented to indicate to the reader the wide variety of micro-organisms available for interaction with the organic chemicals and methods for identifying their presence and diversity. The main emphasis in this chapter is on the biological treatment of contaminants. Various types of organisms involved will be described, and growth and metabolism of bacteria, in particular, will be emphasized. The types of chemicals that can be biodegraded or transformed, and the pathways of conversion are discussed as well as the toxicity and availability of several chemicals. A proper understanding of these aspects is very important because they will serve as the foundation of knowledge required for determining the potential for natural attenuation, and especially those facets dealing with natural bioremediation.