Biofilm is an integral element of the ecosystem in each device of the technological process in wastewater treatment plants (WWTP). Until now, no comprehensive analysis of the occurrence of morphological groups in the biofilm of wastewater treatment devices has been performed. Wanting to fill this gap, the aim of the present article was to determine the structure of the biofilm in the technological system of a WWTP in Lublin (Poland). Abundance of individuals from the following morphological groups was assessed: fungi, flagellates, algae, testate amoebae, ciliates, rotifers, and nematodes. Additionally, values of three biocoenotic indices were determined, that is, the Shannon Diversity, McIntosh Evenness, and Berger–Parker (dominance). Results have demonstrated differences in the structure of the biofilm between the devices. Flagellates and fungi dominated in the mechanical part, whereas the biological elements were dominated by ciliates, amoebae, and rotifers and the treated wastewater by algae and ciliates. Indices indicated the simplest biofilm structure (the lowest biodiversity) at the mechanical stage and at site of discharge of treated wastewater to the receiver. Knowledge of the biofilm structure may be useful for assessment of conditions prevailing in wastewater treatment devices. Moreover, it can be a starting point to develop a quick and low-cost bioindication method applicable in all devices, which can be complementary to standard physicochemical methods.