Compared to other ecosystems, estuarine ecosystems have distinct carbon flux dynamics – the lateral carbon flux incurred by tidal activities, and methane generation under the anaerobic conditions of wetland soils. The conventional estimation of gross primary production (GPP) based on the light use efficiency (LUE) model used for non-wetland terrestrial ecosystems, therefore, cannot be applied directly to estuarine wetland ecosystems. In this paper, we estimated the 2005's annual carbon budget of an estuarine wetland on Chongming Island, Shanghai, and partitioned the losses of carbon due to lateral tidal dynamics and anaerobic methane production using an innovative technique. The average GPP calculated from eddy covariance between March and November was 261.79 μmol m−2 day−1, whereas that from the LUE model was 58.84 μmol m−2 day−1. The correlation coefficient between GPP simulated from the LUE model and that calculated from flux tower data was low in the growing season (R2=0.55). We hypothesized that tidal activities and uncounted methane release were responsible for the difference, which can be predicted from measurements of remote sensing products such as land surface water index (LSWI), evapotranspiration (ET), and tide height (TH). We developed an integrated GPP model by combining the LUE model and an autoregression model to estimate carbon budget. The average GPP from the modified model increased to 263.38 μmol m−2 day−1, and R2 for the correlation between the simulated and calculated data increased to 0.88, demonstrating the potential of our technique for GPP estimation and quantification of seasonal variation in estuarine ecosystems. The approach developed in this study has great potential for correcting unavoidable errors when estimating carbon budget of coastal wetlands. Furthermore, global warming is expected to accelerate sea level rise, which may enhance the effect of tidal activities and increase the difficulty in estimating coastal carbon budgets using conventional methods.