ABSTRACT: Estuarine and coastal wetlands have great potential as carbon sinks; however, the carbon fluxes of unvegetated tidal flats remain unclear. The CO2 flux of tidal flats is mainly controlled by CO2 uptake by microphytobenthos (MPB) and CO2 emission by sediment respiration. In this study, a brackish tidal flat (B-TF) and freshwater tidal flat (F-TF) in the Yangtze Estuary were selected to investigate the effects of salinity on microphytobenthic growth (indicated by the content of chlorophyll a and pheopigment) and the CO2 flux of tidal flats (during daytime). The results showed that the sediment salinity at B-TF was 5–19 times higher than that at F-TF depending on the season. Diatoms showed a dominant salt water community at B-TF and a freshwater community at F-TF. Over spring, autumn and winter, CO2 absorbed by MPB was on average 113% and 230% of the CO2 emitted by sediment respiration for B-TF and F-TF, respectively, showing a CO2 sink capacity. High salinity in winter inhibited sediment respiration and improved the physiological status of the MPB, making the B-TF a strong CO2 sink, whereas the F-TF was a strong CO2 sink in summer. The fresh water and dissolved silicon (SiO32-) input to the estuary via the river had significant effects on MPB growth and sediment respiration, which were also influenced by light, temperature, and pH. Our study highlighted the importance of estuarine salinity fluctuations in the CO2 sinks of estuarine tidal flats, which should be given additional attention when assessing the role of tidal flats in CO2 mitigation.