Inland aquatic systems are active components of the carbon cycle, with organic matter production and consumption in these waters serving as conversion mechanisms for carbon. The standard method for measuring metabolism in running waters, the open-channel method, depends on an estimated diffusion coefficient that causes some uncertainty in the measurements. The aquatic eddy correlation technique measures benthic fluxes based on simultaneous measurements of vertical flow velocity and the oxygen concentrations associated with this flow a short distance above the sediment surface and may be a preferred alternative to the open channel method. We designed an optode-based eddy correlation system that measures benthic oxygen fluxes in shallow running waters and compared the measurements from this system to those made with the open-channel method. We will use the results of these measurements to recommend metabolism measuring procedures in running water and to answer questions about the fate or organic matter in Colorado plains rivers.