Restored wetlands are a complex mosaic of open water and new and old emergent vegetation patches, where multiple environmental and biological drivers contribute to the measured heterogeneity in methane (CH4) flux. In this analysis, we replicated the measurements of CH4 flux using the eddy covariance technique at three tower locations within the same wetland site to parse the spatiotemporal variability in CH4 flux contributed by large-scale seasonal variations in climate and phenology and short-term variations in flux footprint movement over a mosaic of vegetation and open water. Using a hierarchical statistical model accounting for site-level environmental effects, tower-level footprint and biological effects, and temporal autocorrelation, we partitioned the key drivers of the daily CH4 flux variability among the three replicated towers. The daily mean air temperature and mean friction velocity, a measure of momentum transfer, explained a significant variability in CH4 flux across the three towers, and the abundance and spatial aggregation of vegetation in the flux footprint along with the daily gross primary productivity explained much of the tower-level variability. This statistical model captured 67% of the total variance in the daily integrated growing season CH4 fluxes at this site, which bridged an order of magnitude from 80 to 480 mg C m−2 d−1 during the measurement period from 10 May 2012 to 24 October 2012.