Freshwater lakes are important for drinking water, fisheries and have high societal significance as recreational areas. Ammonium accumulation would endanger these ecosystem services. At the same time, ammonium is an important constituent of agricultural fertilizers and its concentrations in the environment have increased dramatically with the consequence that the global nitrogen cycle has long exceeded safe operational boundaries. Using state-of-the-art methods in environmental systems microbiology (amplicon sequencing, metagenomics, metatranscriptomics) and biogeochemistry (stable isotope-based rate measurements), we study bacterioplankton dynamics, toxic cyaonobacterial blooms, sediment microbiomes and ammonia-oxidizing microorganisms in the background of climate change and steadily increasing water temperatures in lakes.