A major objective of biogeochemical studies of coral reefs is to quantify fluxes of particulate and dissolved matter between the reef and overlying waters. However, direct measurements of these fluxes are hard to obtain due to the typically small concentration changes as the water flows over the bottom and due to shear, turbulent mixing and concentration gradients characterizing benthic boundary layers. Using state-of-the-art underwater technology, we were able to apply the “Control Volume” approach to measure in situ phytoplankton grazing on a scale of a whole coral reef community. The results indicate that the import of carbon and nutrients via this grazing is a major, previously underestimated, trophic pathway in coral reefs. The amount of phytoplankton grazed by 1 m2 of reef is similar to the total phytoplankton produced in the entire water column of the surrounding sea under 1 m2 of sea-surface. The import of allochthonous nutrients into the reef via this grazing balances the downstream leak of dissolved nutrients. Physically, the flow over the rough topography of the reef produces enhanced turbulence, enabling high grazing rates to be sustained, while on larger scales, the exchange between the offshore ocean and the reef is supported by buoyancy-driven flows. With the advent of underwater technology, the control volume technique is no longer limited to unique situations (e.g. closed lagoons, shallow flats), but should be generally applicable for measurements of benthic-pelagic fluxes in oceans and lakes.