Lake littoral zones have a transitional nature and dynamic conditions, which are reflected in their CH4 emissions. Thus, detailed studies are needed to assess the littoral CH4 emissions in a regional scale. In this study, CH4 fluxes were followed during the ice-free seasons in 1998 and 1999 by using the static chamber method in the littoral zone of two lakes in Finland. An exceptionally high water level in 1998 caused an unusually long inundation in otherwise ephemerally flooded zone. The flooding was normal in year 1999. The factors controlling CH4 emissions were examined and statistical response functions were constructed. Further, the effect of extended flooding on the littoral CH4 budged was estimated. The methane flux was primarily regulated by the water level in grass and sedge dominated eulittoral zone, but not in infralittoral reed and water lily stands. Methane emissions in the sedge dominated zone decreased significantly, when the flood was high enough to submerge the venting structures of the plants. Besides water level, sediment temperature determined CH4 emission. The cumulative CH4 emissions from the whole littoral wetlands in wet year were 1.1 times (L. Kevätön), or 0.61 and 0.79 times (L. Mekrijärvi) those in dry year. The crucial factor was the discrepancy between the exceptional and the average water level. The extension of inundated area does not necessarily increase CH4 emissions if the flood reaches infrequently inundated areas, which apparently have low CH4 production potential. This is the case especially, if the emissions in lower zones simultaneously decrease due to high water level. Our study analyses these complex responses between CH4 emissions and water level.