To understand how hydrological processes affect biogeochemical and methane (CH4) cycles in temperate riparian wetlands, we measured CH4 fluxes and dissolved chemical constituents and CH4 concentrations in groundwater, and monitored several environmental factors in wetlands located within a forested headwater catchment in a warm, humid climate in Japan. Variation in redox components dissolved in groundwater, including nitrate (NO3 -), Mn, Fe, and sulfate (SO4 2-), depended on temperature and soil-water conditions. Strongly reducing conditions usually occurred in the high-temperature months of July, August, and September. Dissolved CH4 in groundwater changed with redox conditions and was highest in summer and lowest in winter. CH4 emissions from riparian wetlands were observed almost throughout the year and displayed clear seasonality. Occasionally in summer, emission rates were more than 4 orders of magnitude greater than hillslope uptake rates. Although CH4 emissions increased markedly during most of the summer, they were constrained by (1) fluctuation of the water table, which when lowered can shift the subsurface zone to a more oxidized condition, and (2) the oxygen-rich water such as precipitation and lateral subsurface flow from the hillslope. These results suggest that hydrological processes in forest headwater catchments play an important role in supplying oxygen to soils and consequently affect biogeochemical cycles, including CH4 formation, and that small wetlands in forest watersheds function as large sources of CH4, especially in regions with warm humid summers.