The complexity of environmental systems such as sediments requires a multifaceted approach to understand microbial processes. For a long time microbial processes have been studied in microcosms using analytical tools that ignore the complexity and the diversity of microbes in conjunction with the local environmental matrix. Recent developments in molecular biology and genomics are offering tools to explore microbial processes at a level that encompasses the molecular genetic characteristics of the local microbial players, culturable or not, as well as their organization into complex communities and their interactions both with each other and with the target chemicals. It is now possible to study microbes directly in their environments at the population level as well as at the single cell level. The presentation will outline the recent developments in the detection and monitoring of microbial processes in polluted sediments.