The Water Frame Directive 2000/60/CE underlines the importance of sediments and requests the creation of a European net (SedNet) for their management. Sediments play an important role for the river basin and offer a variety of habitats to many aquatic organisms. Microorganisms, such as Clostridia, are indispensable for a lot of symbiotic and pathogenic relationships with higher organisms and the disappearance of these communities could cause extinction of many species. Thus, Clostridia communities represent the most suitable microbiological indicators to characterize the ecological quality of sediments. The creation of SedNet may make it possible to develop a series of best recommendation in sediment management.