The project focuses on investigating the functional and geochemical roles of microbial biofilms in freshwater karst ecosystems, aiming to understand their involvement in biogeochemical cycles and extracellular enzymatic activity. The research is conducted in two climatically contrasting areas of Croatia – Plitvice Lakes National Park and Krka National Park – in order to compare microbial processes and their relationship with environmental factors. The project includes field sampling, laboratory analyses, and the application of molecular and metagenomic approaches. The functional activity of microbial communities is assessed using the Biolog EcoPlates™ system and fluorimetric methods, while structural diversity and genetic potential are examined through amplicon and metagenomic sequencing. The obtained data are processed and interpreted using advanced statistical and bioinformatic tools in the R programming environment, integrating functional and environmental parameters. As part of the project, scientific training is being carried out at the Probst Lab (Germany), a leading European centre for aquatic microbiome research. During this training, existing datasets are being integrated with new multi-omics analyses (metagenomics, metatranscriptomics, metaproteomics, lipidomics), and bioinformatic protocols are being developed for the analysis and visualization of multi-layered data. The project contributes to advancing the understanding of microbial functional ecology in karst aquatic systems and to strengthening methodological and analytical capacities in the field of environmental microbiology in Croatia.