Coastal fjords are sensitive ecosystems that integrate signals from natural processes and human activities occurring across their catchments. Fjord sediments act as long-term sinks for organic matter, nutrients, pollutants, and microorganisms, making them particularly suitable for studying cumulative environmental impacts. This project applies shotgun metagenomics to characterise microbial community composition, functional potential, and functional gene diversity in sediment samples collected along an environmental gradient in a Danish fjord. Approximately 25 sediment samples will be analysed, each sequenced at 6–12 GB per sample. Metagenomic data will be processed using established, community-maintained workflows. The nf-core/mag pipeline will be used for quality control, de novo assembly, metagenome-assembled genome (MAG) reconstruction, taxonomic classification, and genome-resolved functional annotation. This enables the recovery of dominant microbial populations and the identification of metabolic pathways related to biogeochemical cycling, including nitrogen, sulfur, and carbon transformations. To complement genome-resolved analyses, nf-core/funcscan will be applied to screen unassembled and assembled metagenomic data for functional genes of environmental relevance. This includes genes associated with nutrient cycling, stress responses, antibiotic resistance, and mobile genetic elements. Functional profiling will allow quantitative comparisons of gene abundances across the fjord gradient and support the identification of potential signatures of anthropogenic influence, such as wastewater-derived functional markers. By integrating MAG-based analyses with comprehensive functional gene screening, the project will assess how microbial community structure and functional capacity vary spatially within fjord sediments. The results will provide high-resolution insights into sediment microbial ecology and demonstrate the use of reproducible, scalable metagenomic workflows on national high-performance computing infrastructure.