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Abstract: Various physical and biological factors control the processing of materials in aquatic ecosystems. Metabolic processing related to microbial diversity, the presence of aquatic plants, and ecosystem shape combined with other physical and climatic features will be discussed across different aquatic ecosystem types. What is the role of microbes in the long-term burial of carbon in areas with deep vertical mixing in the ocean? How much nitrogen can macrophyte meadows remove in a large river and how does climate influence this capacity? Can we determine a land-use development to sustain the water quality of lakes based on their individual shape? By exploring the complex nature of ecosystem processing in these diverse examples, we better understand the challenges related to the ways in which humans account for regulatory ecosystem services for long term sustainability.