This output presents an updated and harmonized framework for sediment sampling, aimed at improving the quantitative and qualitative analysis of sediments from large and complex aquatic ecosystems, in particular from the Danube River Basin. It builds on initiatives from previous projects, such as the SIMONA project, but also on ISO standards for sediment and water sampling (e.g., the ISO 5667 series). The document brings methodological improvements based on the authors’ practical field experience, on inter-institutional collaboration between several Danube countries, and on the scientific literature consulted. The sediment and water sampling strategy, site selection, methods and equipment, and sampling frequency, as well as the transport and stabilisation of collected samples, are addressed from a field practice perspective, including updated recommendations on the investigation of chemical, physical, biological, and microbiological properties of sediments, with a special focus on emerging pollutants such as microplastics. The focus is on taking into account hydromorphological variability and biological indicators and on improving monitoring in areas affected by anthropogenic activity and climate change. By promoting consistency and comparability between monitoring efforts, this document supports more effective sediment2management and the implementation of policies in line with the Water Framework Directive and other EU environmental regulations.