We report on direct measurements of net ecosystem productivity (NEP) and net ecosystem calcification (NEC) in a Florida Bay seagrass ecosystem. We found notable differences between our carbon-based NEP and similar determinations made using oxygen. Over the study period, both NEP and NEC were negative, revealing that these sites are net heterotrophic and have dissolved CaCO₃. Our findings point to sediments maintaining negative NEP and NEC despite high seagrass above-ground primary production.