Dissolved inorganic carbon, dissolved oxygen, H+, and alkalinity fluxes from permeable carbonate sediments at Heron Island (Great Barrier Reef) were measured over one diel cycle using benthic chambers designed to induce advective pore-water exchange. A complex hysteretic pattern between carbonate precipitation and dissolution in sands and the aragonite saturation state ($Ømega$Ar) of the overlying chamber water was observed throughout the incubations. During the day, precipitation followed a hysteretic pattern based on the incidence of photosynthetically active radiation with lower precipitation rates in the morning than in the afternoon. The observed diel hysteresis seems to reflect a complex interaction between photosynthesis and respiration rather than $Ømega$Ar of the overlying water as the main driver of carbonate precipitation and dissolution within these permeable sediments. Changes in flux rates over a diel cycle demonstrate the importance of taking into account the short-term variability of benthic metabolism when calculating net daily flux rates. Based on one diel cycle, the sediments were a net daily source of alkalinity to the water column (5.13 to 8.84 mmol m−2 d−1, depending on advection rates), and advection had a net stimulatory effect on carbonate dissolution. The enhanced alkalinity release associated with benthic metabolism and pore-water advection may partially buffer shallow coral reef ecosystems against ocean acidification on a local scale.
