Floods control greenhouse gas (GHG) emissions in floodplains; however, there is a lack of data on the impact of short-term events on emissions. We studied the short-term effect of changing groundwater (GW) depth on the emission of (GHG) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in two riparian grey alder (Alnus incana) stands of different age in Kambja, southern Estonia, using the opaque static chamber (five replicates in each site) and gas chromatography methods. The average carbon and total nitrogen content in the soil of the old alder (OA) stand was significantly higher than in the young alder (YA) stand. In both stands, one part was chosen for water table manipulation (Manip) and another remained unchanged with a stable and deeper GW table. Groundwater table manipulation (flooding) significantly increases CH4 emission (average: YA-Dry 468, YA-Manip 8,374, OA-Dry 468, OA-Manip 4,187 μg C m−2 h−1) and decreases both CO2 (average: OA-Dry 138, OA-Manip 80 mg C m−2 h−1) and N2O emissions (average: OA-Dry 23.1, OA-Manip 11.8 μg N m−2 h−1) in OA sites. There was no significant difference in CO2 and CH4 emissions between the OA and YA sites, whereas in OA sites with higher N concentration in the soil, the N2O emission was significantly higher than at the YA sites. The relative CO2 and CH4 emissions (the soil C stock-related share of gaseous losses) were higher in manipulated plots showing the highest values in the YA-Manip plot (0.03 and 0.0030 % C day−1, respectively). The soil N stock-related N2O emission was very low achieving 0.000019 % N day−1 in the OA-Dry plot. Methane emission shows a negative correlation with GW, whereas the 20 cm depth is a significant limit below which most of the produced CH4 is oxidized. In terms of CO2 and N2O, the deeper GW table significantly increases emission. In riparian zones of headwater streams, the short-term floods (e.g. those driven by extreme climate events) may significantly enhance methane emission whereas the long-term lowering of the groundwater table is a more important initiator of N2O fluxes from riparian gley soils than flood pulses.