Methane (CH4) is a powerful and yet poorly constrained greenhouse gas flux from peatlands. There is a need for studies that can further our biogeochemical understanding of how water table fluctuations affect production and transport of this gas. Swamps, an important but understudied peatland type in Canada, are characterized in part by their seasonal water table fluctuations. We thus conducted a six-month swamp column experiment to: i) understand how water table fluctuations stimulate and/or inhibit production of CH4, and ii) evaluate the relative contribution of physical and biological mechanisms to the observed lag times and hysteretic patterns. Six peat cores (45 cm deep, 15 cm diameter) were collected from each of two swamps: a boreal swamp in the Hudson Bay Lowlands’ headwaters and a temperate swamp in Southern Ontario. We tracked how 30 cm water table fluctuations affected CH4 fluxes using the closed chamber method and a trace gas analyzer. We periodically sampled pore gas and water CH4 concentrations in the columns. Water table fluctuations increased CH4 emissions compared to the control columns. The two-week lag times between changes in moisture content and CH4 fluxes appear to be driven by transport rather than production limitations. Linear regression analysis did not identify a significant effect of soil moisture content or water table depth on CH4 fluxes, indicating that simple regression approaches may be insufficient to understand complex CH4-hydrologic relationships. This research will improve our mechanistic understanding of CH4 cycling in swamps in Canada, with applications for other peatland types.