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• Coastal ecological and hydrological processes were coupled in a carbon flux model. • Model reproduced well the spatiotemporal dynamics of CO 2 and CH 4 fluxes. • Magnitude of flooding suppression on carbon fluxes was proportional to tidal landform. • Temperature and tidal height explained most of periodic variation of carbon fluxes. • Effects of environmental variables was dependent on marsh elevations and seasons. Carbon exchange in coastal wetlands is a complex biochemical process regulated by a combination of meteorological, plant-soil, and hydrological factors. In the Yangtze Estuary, a process-based carbon flux model was developed to further elucidate the spatiotemporal dynamics of carbon fluxes of different marsh species and elevations, incorporating the roles of climatic, hydrological, and geographical factors. The model was validated based on measurements of CO 2 and CH 4 fluxes using the static chamber and eddy covariance methods. The results showed that the model reproduced well the time series of the net ecosystem change (NEE) and CH 4 flux from diel to half-month scales. During tidal cycling, the ecosystem CO 2 and CH 4 fluxes were suppressed under inundation, and the magnitude of suppression was proportional to the water depth. The landform of the tidal flat determined the submerged height and duration, and the hydrological effects on carbon fluxes varied with elevation. The model also reasonably reflected the negative correlation between tidal height and salinity and carbon fluxes during the spring-neap cycle. Sensitivity tests revealed that temperature and tidal height were the two most critical factors affecting the carbon fluxes. Wavelet coherence analysis further indicated that temperature and tidal height explained most of the periodic variations in NEE at the diel scale. Specifically, temperature dominated CH 4 emission dynamics in spring and winter, whereas tides replaced temperature as the dominant factor in summer. The temperature also exhibited a stronger coherent intensity at high elevations, whereas the influence of tides was greater in low-lying regions. This study emphasizes the associated effects of climatic, biological, and hydrological factors on the spatiotemporal heterogeneity of carbon fluxes in the coastal marshes. This coupled model is expected to be beneficial for estimating the carbon sequestration capacity in China's coastal salt marshes under global change conditions. [ABSTRACT FROM AUTHOR]