Wing-dimorphic insects occur in diverse habitats in heterogeneous environments. However, little is known about the wing dimorphism of insects that inhabit floodplains and the possible environmental factors affecting their wing morphs. In this study, we used cantharidin-baited traps to collect and quantify the psammobiont beetle Mecynotarsus niponicus Lewis, 1895 (Anthicidae) in a sandy floodplain of the Tamagawa River, Japan, in a one-year repeated cross-sectional study design. Our analysis of the demographic characteristics of over 400 M. niponicus adults and public weather-related data showed that: 1) two distinct wing morphs, long-winged (macropterous) and short-winged (brachypterous) individuals, were present within the population; 2) macroptery rates were consistently lower but varied greatly (6.7–50.0%) within a year; and 3) higher macroptery was significantly associated with greater fluctuation in river water level, namely flooding (odds ratio, 2.96; 95% confidence interval, 1.78–4.91; P < 0.001). Thus, the macropterous form of M. niponicus may be advantageous in avoiding temporal habitat loss due to river flooding. These observations may represent a first step toward testing a flooding-dispersal hypothesis for the morph alteration of wing-dimorphic insects in floodplains.