Seasonal changes in the environment often strongly influence biological communities. In environmental transition zones, or ecotone, the environment fluctuates over time between two different types of environments, and the seasonal change is more pronounced. Although emphasis has been placed on the spatial variation of biota along environmental gradients, seasonal change has not been well studied despite the seasonal nature of many ecotones. In this study, we investigated seasonal shift in aquatic community structures of floodplain waterbodies characterized as transitions between lotic and lentic environments, and further investigated the biological processes behind the shift. We observed a clear seasonal shift of community structure in floodplain waterbodies. From the spring snowmelt season to the summer low flow season, the aquatic community structure was largely driven by the hydrological connectivity to the river, represented as the timing of the lotic-lentic transition during the seasonal flood recession. In contrast, after a few months of summer low flow period, the effect weakened over time, and the communities were structured based more on the basis of the local environment. The seasonal shift was largely explained by the change in amphibian and aquatic insect larvae, the main members of the floodplain aquatic assemblage, which metamorphose and emerge from the water during the summer period and then re-distribute in different ways more strongly influenced by local environmental factors such as water body size, temperature, and dissolved oxygen levels. Given that biota in ecotones occupy the habitat for a limited time due to the severe environmental fluctuations, such seasonal changes as we observed in this study may be widespread in ecotones. Landscape and local environmental conditions could alternately shape community structures in different seasons. Further attention to the temporal aspects of community structure is needed for community studies as well as for conservation.

The survey targeted four faunal groups: plankton, benthos, nekton (fishes), and amphibians. Benthic invertebrates were sampled with Surber net samplers (25 cm ´ 25 cm). Three samples were collected at each site on each sampling date and combined. Benthic samples were immediately sieved through a 0.5 mm mesh and preserved in 99% ethanol for later sorting. Fish were captured with a backpack electrofishing unit (Model 12B, Smith-Root Inc., Vancouver, Washington, USA) using a pulsed direct current setting (300–400V, DC). A crew of two or three study participants sampled in an upstream direction. The entire area of small waterbodies or the first 20–120 m of paleo-side channels at the site longer than 120 m were sampled by the two-pass method. All fish collected in the surveys were identified to species and released back to the same site alive. The fish catch per unit effort was calculated by dividing the fish count by the total habitat area sampled. The density of amphibian larvae was binomial (very high or zero), because their presence depend on whether their adults lay egg-mass, which contains many eggs. Therefore, for amphibians, we recorded presence/absence of their larvae rather than their density by visual investigation during the electrofishing survey. For plankton, 10 L of water was filtered through a 70-μm-mesh plankton net and preserved in 2% Glutaraldehyde for zooplankton analysis.