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Seagrass meadows are productive and functionally important seafloor habitats that are declining in many parts of the world under pressure from human activities. Seabed light availability is inversely related to water depth, thus sea level rise associated with global warming may impinge upon seagrass productivity and its contributions to coastal ecosystems. Across natural variation in seagrass bed depth driven by tidal oscillations and distance from shore, we quantified seafloor oxygen exchange every 15 min for three days and nights at sites in New Zealand using aquatic eddy covariance to better understand the implications of sea level rise on shallow seagrass. Four sites of differing mean depth (1.5–4.0 m deep at high tide) were net producers of oxygen when photosynthetically active radiation at the seabed was >87.5 μmol photons m−2 s−1, with net oxygen production >4 mmol m−2 h−1 at all sites during peak sunlight hours. The effect of light attenuation on dissolved oxygen production was evident when comparing fluxes in the morning (low tide) and evening (high tide), with relatively similar incident light levels arriving at water surface at these times of day. The shallowest site was expected to receive the greatest amount of light at the seabed and be most productive. However, the second shallowest site was the most productive, due to higher seagrass cover and clearer water (less light attenuation in the water column). Higher cover of seagrass likely reduced sediment resuspension while increasing photosynthetic capacity (i.e., more photosynthetic biomass). The existence of turbid fringes of water near the upper shore and climate-related shifts in suspended sediment concentrations may interfere with predictions of shoreward migration of seagrass meadows, which are already complicated by interactions with upper intertidal vegetation (e.g., mangroves) and human built structures (e.g., seawalls). • Ecosystem scale seagrass primary production was assessed in a tidal estuary. • Aquatic eddy covariance method elucidated irradiance-photosynthesis relationships. • The shallowest site did not have highest seabed light due to a turbid fringe. • Seagrass production across the large meadow was highest during low tide. • Sea level rise and turbidity may interactively affect future seagrass distribution. [ABSTRACT FROM AUTHOR]