Human dependence on freshwater ecosystems for agriculture and drinking water is well known, though these habitats account for only 0.01% of Earth's water. As this dependence intensifies, rivers and streams are increasingly faced with stress from multiple sources, e.g., urbanization, agricultural practices, global warming and industrial pollutants which impact organisms vital for ecosystem functioning. Microorganisms and macroinvertebrates are one of the key drivers in maintaining a healthy freshwater ecosystem through nutrient cycling and carbon flow. They degrade organic matter and support directly or indirectly a wide array of other organisms within the food web. Given the important role asserted by microbial communities in supporting ecosystem functioning, their ubiquity, and high diversity, they constitute a promising tool for biomonitoring, as changes in microbial community composition and function might reflect different impacts from anthropogenic stressors. Thanks to advances in technology such as Illumina and Nanopore sequencing, alongside comprehensive taxonomic databases and clustering algorithms such changes could be monitored. However, current methods largely lack streamlined bioinformatic pipelines yielding reproducible results. In response, we developed the bioinformatics pipeline Natrix2, capable of analyzing both Illumina and Nanopore amplicon data. This pipeline includes databases for Protists (PR2), bacteria (SILVA), and fungi (UNITE), and incorporates VSEARCH as an alternative to SWARM for clustering. We also implemented error correction steps to enhance the analysis of Oxford Nanopore Technologies (ONT) sequencing data. Our pipeline aims to streamline amplicon data analysis and improve reproducibility. In comparing Nanopore with Illumina sequencing, which is the gold standard for metabarcoding, we demonstrated that ONT 18S sequencing, with Natrix2 error correction, offers a viable alternative for species-level taxonomic resolution. The identification of environmental contaminant-sensitive species Planothidium frequentissimum and Cocconeis placentula highlighted Nanopore 18S sequencing as a potent alternative tool for biomonitoring. We thus applied the Natrix2 pipeline as a biomonitoring tool to examine the impact of multiple stressors (increased salinity, increased temperature, and reduced flow velocity) on ecosystem functions like organic matter degradation and predator prey interactions by microbial community. More specifically, we focused on fungal and bacterial contributions to leaf litter degradation in river sediment. Sediment community analysis revealed that dominant phyla in both terrestrial and aquatic habitats for organic matter degradation were similar. Moreover, by analyzing the metatranscriptome, we found that these microbial groups exhibited similar degradation-related gene expression, indicating synergistic functional interactions. The microbial community plays a crucial role in organic matter degradation and also facilitates the flow of carbon and nutrients through the ecosystem via predator-prey interactions, exemplifying a key aspect of top-down control. Exploring top-down control of microbes, such as bacteria by protist grazers, we assessed the impact of salinization and heat stress on predator-prey interactions between heteronanoflagellates (HNFs) and bacteria in the pelagic zone (water column). Results indicated that salinity strongly affects water column’s microbial community, shifting bacterial and HNFs populations and altering HNFs food selection. These findings underscore that disturbances in HNFs predation can disrupt bacterial community composition, impacting microbial dynamics and resulting in changes in ecosystem functions such as organic matter degradation. Building on these insights in pelagic microbial interactions, we further investigated the effects of stressors on benthic communities and their recovery, examining how bacterial populations adapt to and recover from increased temperature, salinity, and reduced velocity. Utilizing amplicon, metagenome, and metatranscriptomic datasets, this multi-omics study highlighted reduced velocity as a primary driver of sediment bacterial community shifts. In comparison to water column communities, sediment bacteria seemed less affected by salinity. In terms of functional gene expressions, the Chaperone genes were upregulated, marking microbial stress under stressor conditions. Furthermore, as part of a broader investigation into organism groups and ecosystem functions, we assessed the impact of reduced velocity and increased salinity on macroinvertebrates, fungi, algae, and ecosystem functions such as primary production and organic matter degradation. Reduced flow velocity significantly altered macroinvertebrate community composition and slowed organic matter decomposition rates. In contrast, salinity had minimal effects, possibly due to historical coal mining and wastewater influences. Collectively, the studies in this thesis illustrate the critical role of microorganisms and macroinvertebrates in ecosystem functions like organic matter degradation and predator-prey interaction, elucidate how anthropogenic stressors impact these communities and ecosystem functions, ultimately influencing the health of freshwater systems.