Cobble-bar vegetation is maintained by moderate frequent disturbances of moderate floods, which prevent plant succession. However, in the river altered by flow control, land-use conversion for agriculture and urban development, infrequent, large disturbances may completely clear seed sources. The existences of flood refugia allow plant species to survive large floods. Therefore, understanding how refugia are established is essential for the successful protection and restoration of the plant community, including local plant endemic species. We have identified the location of the refugia in a mid-reach at Ibogawa River in Japan after a decade-long observation study of the vegetation dynamics. Here the bed shear stress, which represents the disturbance intensity, was estimated by two-dimensional analysis (2D) and large-eddy simulation (LES). Around the bar’s front line, where the flow bends sharply, the LES reproduces the secondary flow better than the 2D analysis. However, in other areas, both methods perform equally. At the cobble bar downstream tip, in particular, which includes the refuge site, the bed shear stress of both analyses did not exceed the critical value, even during large floods. Comparing the numerical flood-flow simulations of the straight river reach (with an embankment) with those of the curved one (without an embankment) revealed that the flood refuge is estblished by four terrain factors: a secondary bypass channel, a mound in the bar’s center, a sharp bend, and a wide channel. These morphological results offer effective guidelines to conservation planning of the cobble-bar vegetation.