The water quality protection function of riparian buffers is widely recognized, but much less is known regarding the dynamics of greenhouse gases in these ecosystems. Carbon dioxide (CO2) and methane (CH4) fluxes were monitored at 6 riparian sites along a 4th-order segment of the White River (Indiana, USA) to assess the effect of vegetation and flood frequency on gas fluxes. The study sites included shrub/grass, young (<15years) and mature (>80years) riparian forests that were either flood-protected (FP), occasionally flooded (OF) or frequently flooded (FF). No significant effect of vegetation type on either CO2 or CH4 flux was noted. While CH4 level was sometimes high (up to 120μLL−1) in the deep soil layers, concentration near the soil surface (1.28μLL−1) was generally lower than in the litter layer (2.35μLL−1). In addition to this pattern, the negative relationship (r2: 0.23, P<0.04) between CH4 flux and soil air CH4 concentration in the 0–20cm soil depth suggests the occurrence of a zone of active CH4 oxidation in the upper soil layers. While CO2 emission was significantly (P<0.001) higher at the flood-impacted than at the flood-protected sites, the opposite was observed with regard to CH4 uptake. Depending on soil temperature, flood events triggered spikes in CH4 emission (up to +45.1mg CH4-Cm−2d−1 at the FF mature forest). Among the mature forests, mean flux was +0.61, −1.57 and −3.12mg CH4-Cm−2d−1 at the FF, OF and FP site, respectively. These results demonstrate that some riparian forests can act as strong terrestrial CH4 sinks, but that potential can be easily offset with increased frequency of flooding. Thus, a characterization of flood frequency is required for large scale assessments of CH4 fluxes in riparian ecosystems.