AbstractThe net ecosystem productivity (NEP) of two seagrass meadows within one of the largest seagrass ecosystems in the world, Florida Bay, was assessed using direct measurements over consecutive diel cycles during a short study in the fall of 2018. We report significant differences between NEP determined by dissolved inorganic carbon (NEPDIC) and by dissolved oxygen (NEPDO), likely driven by differences in air–water gas exchange and contrasting responses to variations in light intensity. We also acknowledge the impact of advective exchange on metabolic calculations of NEP and net ecosystem calcification (NEC) using the “open-water” approach and attempt to quantify this effect. In this first direct determination of NEPDIC in seagrass, we found that both seagrass ecosystems were net heterotrophic, on average, despite large differences in seagrass net above-ground primary productivity. NEC was also negative, indicating that both sites were net dissolving carbonate minerals. We suggest that a combination of carbonate dissolution and respiration in sediments exceeded seagrass primary production and calcification, supporting our negative NEP and NEC measurements. However, given the limited spatial (two sites) and temporal (8 d) extent of this study, our results may not be representative of Florida Bay as a whole and may be season-specific. The results of this study highlight the need for better temporal resolution, accurate carbonate chemistry accounting, and an improved understanding of physical mixing processes in future seagrass metabolism studies.