The microfauna in activated sludge deriving from two different wastewater treatment plants has been compared. Investigations were conducted during the period of seven months taking into account the seasonal changes of microfauna. One studied plant received mainly industrial (70%) and some part of domestic (30%) sewage, and the other mainly domestic sewage (90%). The aim was to compare both plants in terms of occurrence and abundance of key group of microfauna. The determination of key groups and taxa along with biodiversity indices showed that they have potential value as indicators of different conditions characteristic for both types of plants. The innovative using of biotic indices in biodiversity studies also provides useful information on plant operating conditions and performance.