Calcium carbonate (CaCO₃) sediments are the dominant form of CaCO₃ on coral reefs accumulating in lagoon and inter-reefal areas. Owing to their mineralogy and a range of physical parameters, tropical CaCO₃ sediments are predicted to be more sensitive to dissolution driven by ocean acidification than the skeleton of living reef organisms. How this scales up to impact infaunal organisms, which are an important food source for higher trophic levels, and thereby ecosystem functioning, is not well explored. We combined seasonal field surveys in a shallow-reef lagoon ecosystem on the Great Barrier Reef, Australia, with stable isotope analyses and a tank-based experiment to examine the potential top-down influence of the deposit-feeding sea cucumber, Stichopus herrmanni, on this infaunal community under current and future ocean pH. Densities of surface-sediment meiofauna were lowest in winter and spring, with harpacticoid copepods (38%) and nematodes (27%) the dominant taxa. Stable isotope analyses showed that S. herrmanni had a top-down influence on meiofauna and microphytes with a distinct δ¹³C and δ¹⁵N trophic position that was homogenous across seasons and locations. Tanks that mimicked sandy shallow-reef lagoon habitats were used to examine the effects of ocean acidification (elevated pCO₂) on this trophic interaction. We used outdoor control (sediment only) and experimental (sediment plus S. herrmanni) tanks maintained at present-day and near-future pCO₂ (+ 570 µatm) for 24 days, which fluctuated with the diel pCO₂ cycle. In sediment-only tanks, copepods were > twofold more abundant at elevated pCO₂, with no negative effects documented for any meiofauna group. When included in the community, top-down control by S. herrmanni counteracted the positive effects of low pH on meiofaunal abundance. We highlight a novel perspective in coral reef trophodynamics between surface-sediment meiofauna and deposit-feeding sea cucumbers, and posit that community shifts may occur in shallow-reef lagoon habitats in a future ocean with implications for the functioning of coral reefs from the bottom up.