AbstractBenthic and pelagic processes are closely coupled in shallow‐water estuarine and marine environments and in lakes yet benthic–pelagic coupling is difficult to simulate in mesocosms. Realistic water column (WC) and bottom turbulence often are not simultaneously mimicked in mesocosm experiments, leading to artifacts and omitting direct and indirect linkages and feedbacks between the sediment and the WC. The information on benthic–pelagic coupling mesocosm studies assembled illustrates the importance of realistic physics in mesocosms. Mesocosm approaches including both WC turbulence and bottom turbulence that are appropriately designed to resemble natural conditions can provide a deeper mechanistic understanding of feedback processes associated with biogeochemical, food web, and the habitat shifts necessary for models, and will help identify cause‐and‐effect relationships. Benthic–pelagic mesocosm experiments with realistic WC and bottom turbulence may fill the large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the WC. Future applications of such benthic–pelagic coupling mesocosm studies are outlined.