This chapter focuses on below-ground bioremediation of contaminants, where the authors explore the tools that allow them to understand and manage the agents of environmental repair – the micro organisms. Metabolism is the term used to describe the chemical transformations that occur within the cell to maintain life. Contaminant biotransformation and degradation in the subsurface are directly dependent on biogeochemical carbon and energy cycles that are facilitated by microorganisms. The biological pathways and biomarker analysis identified putative biological degradation pathways for the primary contaminants based on the relative presence or absence of 16S biomarkers for bacteria that have a demonstrated capability to produce enzymes involved in degradation. The solid portion contains both inorganic and organic material, with the inorganic material ranging in size from clays and silts to sand, gravel, and rocks. The groundwater under a specialty chemical manufacturing plant was discovered to be contaminated with chlorobenzenes.