Rivers and streams provide essential ecosystem services such as drinking water supply, nutrient cycling, and biodiversity support. However, human activities have severely degraded freshwater ecosystems, particularly through chemical pollution. Polar organic micropollutants—including pharmaceuticals, personal care products, pesticides, and industrial chemicals—are of growing concern because they can persist in aquatic environments even after wastewater treatment and may pose risks to both ecosystems and human health. Biodegradation driven by microbial communities is one of the most important pathways for removing micropollutants. Yet, our ability to predict or optimize biodegradation remains limited, largely because we lack detailed understanding of how environmental conditions, habitat heterogeneity, and ecological engineering solutions influence microbial community structure and function. Constructed wetlands (CWs) offer a promising nature-based approach to enhance micropollutant removal, but the microbial assemblages responsible for these processes have rarely been examined at high resolution. This project aims to assess the added value of constructed wetlands for improving micropollutant attenuation and to investigate how habitat heterogeneity and plant–microbe interactions shape microbial communities in both CWs and receiving rivers. To achieve this, we will combine in-situ sampling, laboratory batch incubations, and amplicon sequencing (16S rRNA) to characterize microbial diversity, identify community differences between systems, and evaluate biodegradation potential. Computational resources are required for processing and analysing amplicon sequencing datasets, including quality filtering, denoising, taxonomic assignment, diversity analyses, and multivariate statistical comparisons. The project will generate multiple sequencing runs across several sites, making access to high-performance computing essential for efficient and reproducible analysis.