Minerotrophic sedge fens are common in sub-arctic regions and are a significant source of atmospheric methane (CH₄), yet they have received less attention than other peatlands, such as boreal ombrotrophic bogs, which are smaller sources of CH₄. At the process level, CH₄ fluxes in sub-arctic systems are limited primarily by cold temperatures, and thus are sensitive to potential climate change. This study examined CH₄ dynamics in a temperate sedge-fen to determine controls on the spatial and temporal variability in CH₄ fluxes and, therefore, how the biogeochemistry of CH₄ in sedge-fen peatlands may respond to predicted changes in climate. We used flux chambers and laboratory peat incubations over a six to seven-year period (1994–2000) to study fluxes, pools, and potential production of CH₄ in a peat-forming wetland in central New York State, USA. Results showed that precipitation (i.e., dry years and depth to water table) exerted an important control on annual and seasonal patterns of CH₄ fluxes. Mean summer flux rates ranged from 2258 nmol m⁻² s⁻¹ in the wettest year to −934 nmol m⁻² s⁻¹ (net consumption) in the driest year. CH₄ concentrations in the surface peat were as low as 0.01 μatm and as high as 10 matm in the summer months depending on precipitation patterns. In contrast, CH₄ concentrations were consistently two to three times greater in sub-surface than in surface peat, and pools persisted during dry years and were temporally less variable. Fluxes were only weakly associated with potential CH₄ production rates, which showed little seasonal variation. In-vitro measurements of potential CH₄ production did not sufficiently explain fluxes, suggesting a need for improved in-situ methods for measuring CH₄ production. Site differences associated with different dominant vegetation had a significant effect on CH₄ cycling in all years except the driest, suggesting sensitivity to vegetation changes. These results indicate that predicting responses of fen peatlands to environmental requires an improved understanding of the underlying microbial processes and mechanisms that control CH₄ cycling.