Riverine ecosystems are shaped by hydro, wind, and to a lesser extent geothermal energies, and also through the work of living organisms via photosynthesis and metabolism. Environmental evaluation methods exist to assess environmental health like water quality and quantity, community abundance, and system diversity. However, biotic energy flows, storages, carrying capacities, and respective balances have not been fully explored as an additional and critical environmental health assessment tool. A mechanistic metabolic model was constructed of a small section of the Middle Oconee River (Athens, GA) to predict whole ecosystem properties that can be used to evaluate ecosystem functionality. Model sensitivities to data and assumptions were explored. In the study system, ecosystem biomass and carbon export were found to increase with food web complexity and decomposer trophic transfer efficiency. Metabolic models, currently expanding in larger geographic scale studies, also have robust discovery and educational merit in assessing more localized ecosystems.