Abstract Long-term “blue carbon” burial in seagrass meadows is complicated by other carbon and alkalinity exchanges that shape net carbon sequestration. We measured a suite of such processes, including denitrification, sulfur, and inorganic carbon cycling, and assessed their impact on air-water carbon dioxide exchange in a typical seagrass meadow underlain by carbonate sediments. Contrary to the prevailing concept of seagrass meadows acting as carbon sinks, eddy covariance measurements reveal this ecosystem as a consistent source of carbon dioxide to the atmosphere, at an average rate of 610 ± 990 µmol m -2 hr -1 during our study and 700 ± 660 µmol m -2 hr -1 over an annual cycle. A robust mass-balance shows that net alkalinity consumption by ecosystem calcification explains >95% of the observed carbon dioxide emissions, far exceeding alkalinity generated by net reduced sulfur, iron and organic carbon burial. Isotope geochemistry of porewaters suggests substantial dissolution and re-crystallization of more stable carbonates mediated by sulfide oxidation-induced acidification, enhancing long-term carbonate burial and ultimate carbon dioxide production. We show that the “blue carbon” sequestration potential of calcifying seagrass meadows has been over-estimated, and that in-situ organic carbon burial only offsets a small fraction (<5%) of calcification-induced CO 2 emissions. Ocean-based climate change mitigation activities in such calcifying regions should be approached with caution and an understanding that net carbon sequestration may not be possible.