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Wetlands are the largest natural source of methane (CH4); however, the contribution of subtropical wetlands to global CH4 budgets is still unclear due to difficulties in accurately quantifying CH4 emissions from these complex ecosystems. Both direct (water management strategies) and indirect (altered weather patterns associated with climate change) anthropogenic influences are also leading to greater uncertainties in our ability to determine changes in CH4 emissions from these ecosystems. This study compares CH4 fluxes from two freshwater marshes with different hydroperiods (short versus long) in the Florida Everglades to examine temporal patterns and biophysical drivers of CH4 fluxes. Both sites showed similar seasonal patterns across years with higher CH4 release during wet seasons versus dry seasons. The long hydroperiod site showed stronger seasonal patterns and overall, emitted more CH4 than the short hydroperiod site; however, no distinctive diurnal patterns were observed. We found that air temperature was a significant positive driver of CH4 fluxes for both sites regardless of season. In addition, gross ecosystem exchange was a significant negative predictor of CH4 emissions in the dry season at the long hydroperiod site. CH4 fluxes were impacted by water level and its changes over site and season, and time scales, which are influenced by rainfall and water management practices. Thus with increasing water distribution associated the Comprehensive Everglades Restoration Plan we expect increases in CH4 emissions, and when couple with increased with projected higher temperatures in the region, these increases may be enhanced, leading to greater radiative forcing.