The Long-term Eddy Covariance System (LECS) unites underwater eddy covariance instrumentation with a surface buoy and communications architecture to allow for real-time analysis of benthic DO and H+ fluxes over long time periods. This system enables the better determination of the sinks and sources of DO and H+ in threatened coastal systems, allowing us to understand how their biogeochemical cycles respond to seasonal variability or climatic changes.