Fungi are known to be dominant in terrestrial systems, performing biological breakdown of organic carbon, which is crucial for the carbon cycle. However, their role in the aquatic environment is largely uninvestigated. Different environmental and diversity studies show their presence in a brought spectrum of aquatic habitats and highlight the lack of knowledge of this kingdom. In the last years even a whole new phylum, the Cryptomycota, was discovered and proven to be present in almost every water sample taken. Especially in engineered biological systems, it is crucial to consider the fungal kingdom during investigations to understand and optimize the work considering the whole microbial community. The superordinate objective of this research is to gain insight into and a better understanding of the fungal community in WWTPs in general with a focus on Cryptomycota. To enable this, existing molecular biological methods needed to be adjusted, leading to the development of a specific and reliable qPCR protocol targeting Cryptomycota. After this achievement, the microbial community in down-flow hanging sponge (DHS) reactors is used as a model community to get insight into the abundance and interactions of fungi and other microorganisms involved in wastewater treatment. The reactor performance was analysed and comprehensive quantitative and qualitative (Illumina sequencing) DNA and cDNA studies over reactor height and operation time were carried out. This gives insight into the diversity and abundance of microorganisms. To observe the function of Cryptomycota in those complex communities, correlation analyses are executed.