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Abstract In‐situ, metabolic flux measurements are increasingly being employed in shallow coastal settings to monitor ecosystem health, quantify carbon sequestration and understand biogeochemical cycling more broadly. However, the effectiveness of these techniques in wavy environments with high‐relief roughness remains unclear, as waves and canopy dynamics may modify turbulent mixing. We present measurements of net community production (benthic oxygen flux) from three sites along a wave‐exposed fore reef in Palau, using three different approaches: (a) aquatic eddy covariance, (b) scalar variance, and (c) gradient flux. Results are compared between methods and evaluated across a wide range of mean flow and wave conditions. Eddy covariance measurements were separated into wave‐ and turbulence‐induced fluxes using the Benilov method, a spectral technique commonly used to correct wave bias in momentum flux measurements. Removing wave fluxes from eddy covariance measurements improved agreement between NCP rates at the different sites, suggesting that waves primarily contributed to measurement bias and not to real fluxes for our data sets. With this bias removed, NCP measurements were well correlated across the three methods, even when waves were large relative to mean flows. The primary difficulty in implementing scalar variance and gradient flux methods was identifying the appropriate mixing‐length to parametrize eddy diffusivity. While should be equivalent to the measurement height above the coral substrate, this distance is hard to constrain in environments with nonuniform, canopy‐like roughness such as coral reefs. We discuss challenges and provide recommendations for metabolic flux deployments in shallow coastal environments with waves.