In biological wastewater treatment inorganic and organic substances are fixed and metabolized by mixed populations of microorganisms forming either activated sludge flocs or biofilms. Not only the type of wastewater but also the operational conditions promote the development of an adapted biocenosis of microorganisms with specialized enzymatic functions. Understanding the biological properties of the microorganisms, it is possible to assess the prevailing conditions in their natural environment. Regular microscopic and enzymatic investigations of activated sludge and biofilms thus improve the assessment of the stability of the processes and support troubleshooting in wastewater treatment plants. While the role of bacteria is often discussed, the importance of ciliated protozoes and metazoes for the maintenance of the stability of biofilm systems is rarely mentioned. In this paper we intend to show some new results of direct microscopic observations in different sorts of biofilm systems focussing upon ciliated protozoes and metazoes. Practical results will demonstrate the relation between enzymatic analysis, microscopic investigations and performance of biofilm systems.