Self purification of aquatic systems is one of the most important ecosystem functions and is largely driven by microbial communities. Both, prokaryotes and eukaryotes, have the ability to remove harmful substances from contaminated water or waste streams. Such biological self purification processes are of pivotal importance for drinking water and for waste water treatment. However, variability in ecological microbial parameters is high due to natural and artificial (methodological) variability. Progress in science depends largely on standardised and comparable methods. The reliability and the comparability of published data sets considering that data are based on different methodological approaches shall be discussed. A list of caveats and suggestions for future studies shall emerge (especially concerning the reliability of different methods).