Advanced process understanding of engineered geothermal systems is a prerequisite to optimize plant reliability and economy. In the frame of the MiProTherm project microbial, geochemical and mineralogical aspects of geothermal groundwater systems are investigated. While the main focus of the project is on characterization of indigenous microbial communities and changes of their activity due to plant operation, the monitoring of geochemical and biogeochemical parameters also allows for process analysis. Genetic fingerprinting techniques based on PCR-amplified 16S rRNA- and dissimilatory sulfite reductase genes are used to identify the dominant microorganisms in fluid and filter samples. The identification of microbes and their products enables the correlation to metabolic classes and provides information about the biochemical processes involved. Quantification of microbial activity (qPCR) and physiological characterization of the occurring species will deliver further insight into the role of the different microorganisms and the parameters controlling induced processes. Analysis of phospholipids, indicators of living organisms, enables additional characterization of the microbial community and their adaption to extreme habitats. The microbial monitoring is aimed for early detection of microbial colonization as well as microbial induced corrosion and filter clogging. A timely counteraction against these processes allows an optimization of the geothermal processes used for the energy generation and conservation. The interpretation of shifts in the microbial community composition, correlated with precipitated minerals, will support plant operation under the aspect of problem identification and countermeasures.