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Abstract While a stimulating effect of plant primary productivity on soil carbon dioxide (CO₂) emissions has been well documented, links between gross primary productivity (GPP) and wetland methane (CH₄) emissions are less well investigated. Determination of the influence of primary productivity on wetland CH₄emissions (FCH₄) is complicated by confounding influences of water table level and temperature on CH₄production, which also vary seasonally. Here, we evaluate the link between preceding GPP and subsequent FCH₄at two fens in Wisconsin using eddy covariance flux towers, Lost Creek (US‐Los) and Allequash Creek (US‐ALQ). Both wetlands are mosaics of forested and shrub wetlands, with US‐Los being larger in scale and having a more open canopy. Co‐located sites with multi‐year observations of flux, hydrology, and meteorology provide an opportunity to measure and compare lag effects on FCH₄without interference due to differing climate. Daily average FCH₄from US‐Los reached a maximum of 47.7 ηmol CH₄m⁻² s⁻¹during the study period, while US‐ALQ was more than double at 117.9 ηmol CH₄ m⁻² s⁻¹. The lagged influence of GPP on temperature‐normalized FCH₄(T_air‐FCH₄) was weaker and more delayed in a year with anomalously high precipitation than a following drier year at both sites. FCH₄at US‐ALQ was lower coincident with higher stream discharge in the wet year (2019), potentially due to soil gas flushing during high precipitation events and lower water temperatures. Better understanding of the lagged influence of GPP on FCH₄due to this study has implications for climate modeling and more accurate carbon budgeting.