The Kushiro Mire, the largest mire in Japan, presently faces the serious problem of turbid water flooding. Shortening of stream channels associated with agricultural development is a major cause of streambed aggradation. This aggradation reduces the carrying capacity of the channel, resulting in sediment laden water spilling over the wetlands in a flood event. Sedimentation progresses with repeated inundation by turbid water, which significantly alters the edaphic conditions, and thereby the composition and structure of marsh forests. Aggradation of the geomorphic surfaces with sedimentation lowers the water level, and increases soil particle size and nutrient status. This situation was clearly displayed in an ordination of canonical correspondence analysis. Among the environmental variables, water level was related most strongly to the pattern of a forest community. Salix species dominated the flood areas, which were characterized by a low water level, coarse sediment, and high electrical conductivity. Alnus japonica, the most common tree species in the Kushiro Mire, favors soil conditions represented by high water table and organic content. A. japonica adapts to a higher water level by developing lenticels with hypertrophied and adventitious roots, multiple sprouting and regenerates vegetatively. Basal areas (BAs) of A. japonica, however, seem to be limited by high fluctuations in water levels, which are amplified by channelization. This raises serious concerns for the integrity of the Kushiro Mire. It is important to implement a conservation plan from a watershed perspective because most problems originate in upper basins. Creating riparian buffer strips, sediment-filtering wetlands, and restoring the original meandering course may slow down sedimentation in the mire, and thus help to restore the natural hydrological regime.