Anthropogenic CO2 emissions have altered seawater chemistry causing ocean acidification and affecting the ability of marine calcifiers to build and maintain calcium carbonate structures. Calcifiers such as corals and rhodoliths play key roles in benthic carbon cycling through photosynthesis, respiration, calcification, and dissolution. Despite growing attention to their influence on seawater carbonate chemistry, organism-scale studies in tropical ecosystems, such as the Colombian Caribbean, remain limited. We investigated short-term carbon fluxes by measuring photosynthesis–respiration and calcification–dissolution rates in the coral Siderastrea radians and rhodoliths under natural light at different times of day. In situ incubations at Isla Grande (Corales del Rosario and San Bernardo National Natural Park) showed that both organisms actively modulate seawater carbonate chemistry, but via distinct diel patterns and metabolic strategies. Rhodoliths exhibit highly variable metabolism, with high daytime photosynthesis and pronounced day-night contrasts in calcification, reflecting strong coupling between light, photosynthesis, and CaCO3 precipitation, along with a tendency for nocturnal dissolution. In contrast, S. radians displays lower absolute productivity and calcification rates but maintains metabolic stability through a more regulated coupling of photosynthesis and respiration and a moderated light-to-dark calcification ratio. The higher photosynthesis-to-calcification ratio in S. radians indicates a strategy prioritizing carbon fixation over skeletal accretion, whereas rhodoliths allocate more of their photosynthetic output to CaCO3 deposition than corals. These results highlight the distinct organism-level metabolic strategies and indicate that species-specific patterns of photosynthesis and calcification determine their contributions to short-term carbon fluxes and the surrounding water carbonate dynamics.