Protozoa constitute a major link between the highly productive and nutrient retaining microbial loop and the metazoans of the classical food web. Protozoa are efficient at gathering microbes as food, and they are sufficiently small to have generation times that are similar to those of the food particles on which they feed. They are, in quantitative terms, the most important grazers of microbes in aquatic environments, balancing bacterio-plankton production. Protozoa not only play an important ecological role in the self-purification and matter cycling of natural ecosystems, but also in the artificial system of sewage treatment plants. In conventional plants ciliates usually dominate over other protozoa, not only in number of species but also in total count and biomass. It is generally accepted that their feeding on bacteria improve the treatment, resulting in a lower organic load in the output water of the treated wastes. Due to their biodegradation potential some attempts have been made to use ciliates specifically in environmental biotechnology. As biosensors they could provide valuable information regarding adverse effects of environmental chemicals on this part of the biocoenosis essential for the effective operation of biological waste-water treatment processes.