The role of sediment and epipelon (organisms living on the surface of or in the fine-sized sediments) is significant in the life of aquatic ecosystems. The sediment is the place where the change of ion-transport occurs between the aquatic and solid phases, there are dynamic balance and buffer system between the sediment particles and the particles in the surrounding medium. As a result of the activity of the epipelon and the sediment organisms the metabolism pathways exist in the aquatic ecological systems that can indicate or influence on the habitat characteristics. Changes in the quality or quantity of epipelon indicate changes in water quality. From the point of view of nature conservation it can characterize a natural status or indicate the degree of disturbance (degradation). We measured the ETS (Electron Transport System) activity of the epipelon which gives the maximal intensity of the respiration metabolism. In the analysis of the epipelon the measuring of the ETS-activity can be used of the returns of taxonomic effects such as sublethal or physiologic damage caused by toxic poisons which cannot be discovered immediately and directly by taxonomic parameters, but the changing breath-activity can mark a changing state. ETS tests are suitable for indicating environmental stress