Hydrodynamics of aquatic ecosystems is a relatively new, emerging multidis-ciplinary research area dealing with two key inter-connected issues: (i) physical in-teractions between flow and organisms (e.g., due to drag forces); and (ii) ecologi-cally relevant mass-transfer-uptake processes (e.g., due to molecular and turbulent diffusion). Owing to physical and biological complexity of boundary conditions in aquatic systems, the conventional hydraulic methodologies are often impracticable and new approaches are required. One of such approaches, the double-averaging methodology, is discussed with particular focus on flows over biologically-modified beds.
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