Ocean acidification is a threat to marine ecosystems globally. In shallow-water systems, however, ocean acidification can be masked by benthic carbon fluxes, depending on community composition, seawater residence time, and the magnitude and balance of net community production (NCP) and calcification (NCC). Here, we examine how six benthic groups from a coral reef environment on Heron Reef (Great Barrier Reef, Australia) contribute to changes in the seawater aragonite saturation state (Ω_a). Results of flume studies using intact reef habitats (1.2 m by 0.4 m), showed a hierarchy of responses across groups, depending on CO₂ level, time of day and water flow. At low CO₂ (350–450 μatm), macroalgae (Chnoospora implexa), turfs and sand elevated Ω_a of the flume water by around 0.10 to 1.20 h⁻¹ – normalised to contributions from 1 m² of benthos to a 1 m deep water column. The rate of Ω_a increase in these groups was doubled under acidification (560–700 μatm) and high flow (35 compared to 8 cm s⁻¹). In contrast, branching corals (Acropora aspera) increased Ω_a by 0.25 h⁻¹ at ambient CO₂ (350–450 μatm) during the day, but reduced Ω_a under acidification and high flow. Nighttime changes in Ω_a by corals were highly negative (0.6–0.8 h⁻¹) and exacerbated by acidification. Calcifying macroalgae (Halimeda spp.) raised Ω_a by day (by around 0.13 h⁻¹), but lowered Ω_a by a similar or higher amount at night. Analyses of carbon flux contributions from benthic communities with four different compositions to the reef water carbon chemistry across Heron Reef flat and lagoon indicated that the net lowering of Ω_a by coral-dominated areas can to some extent be countered by long water-residence times in neighbouring areas dominated by turfs, macroalgae and carbonate sand.