With the awareness that the surface ocean is becoming more acidic due to the uptake of anthropogenic CO2 and that the resulting decrease in carbonate ion concentration is contributing to a decline in the calcification rate of many organisms, there is a pressing need to develop methods that can easily and reliably measure the calcification rates of these organisms under natural conditions so that any changes that may be occurring can be detected. Recent advances in control volume  and benthic boundary layer eddy correlation methods [2, 3] promise to make continuous non-invasive measurements of net oxygen community production and respiration a reality. These methods, however, cannot be extended to the measurement of calcification rate because no suitable sensor for the measurement of total alkalinity (TA) exists at the present time. We have a solution that is based on measuring the vertical gradients in current velocity and the chemical constituent of interest in the boundary layer. The vertical gradient in velocity gives us Kz and Kz times δC/δz gives us the flux of constituent C into or out of the seafloor. The method can be applied to the measurement of calcification but could also be applied to the measurement of the flux of any chemical or biological constituent that can be determined from a water sample, in this case O2. Water samples could be collected with an automated water sampler preferably slowly over the period of an hour so that high frequency variability that cannot be sampled would be averaged out. Here we present preliminary data using an Acoustic Doppler Velocimeter (ADV), Modular Acoustic Velocity Sensor (MAVS) and two Aanderaa oxygen optodes. Three test deployments were made on shallow, warm-water coral reefs in La Parguera, Puerto Rico. Time series of net production obtained using the boundary layer gradient flux method (GF) were compared with measurements based on the Eulerian upstream-downstream flow respirometry method and a 1-D water column mass balance method with air-sea gas exchange. The agreement between methods was very encouraging, thus validating the O2-MAVS as an instrument capable of measuring oxygen flux.