A major source of uncertainty in the global methane budget arises from quantifying the area of wetlands and other inland waters. This study addresses how the dynamics of surface water extent in forested wetlands affect the calculation of methane emissions. We used fine resolution satellite imagery acquired at sub-weekly intervals together with a semi-empirical methane emissions model to estimate daily surface water extent and diffusive methane fluxes for a low-relief wetland-rich watershed. Comparisons of surface water model predictions to field measurements showed agreement with the magnitude of changes in water extent, including for wetlands with surface area less than 1,000 m². Results of methane emission models showed that wetlands smaller than 1 hectare (10,000 m²) were responsible for a majority of emissions, and that considering dynamic inundation of forested wetlands resulted in 49–62% lower emission totals compared to models using a single estimate for each wetland’s size.