To elucidate the relationship between biodiversity on gravel islands in a river and flood disturbance characteristics, wash-out conditions of trees and perennial grasses and breaking conditions of trees were analysed and the applicability of these indices was investigated. Two indexes are defined to express breaking and wash-out conditions of trees, breaking or overturning index (BOI) and wash-out index (WOI), respectively, and one index, WOI50, is used to express the removal condition of annual grasses. Using WOI, WOI50, and BOI, this study classified the habitats on gravel islands into five regions. The relationship between the diversity of vegetation area calculated by the vegetation species map in this study, and the flood disturbance index, a kind of probability expectation value of area for each region integrated from 2- to 40-year return periods of floods disturbance, was analysed on six gravel islands in the Arakawa and Tamagawa rivers. Within the five regions (Regions A–E), important trends were found for three regions. The diversity of vegetated areas in the gravel river habitat increased with increasing I d, the flood disturbance index in Region D, which expresses a flood disturbance that can break trees and move medium-size gravel. However, the diversity index has peak values for I a and I e, the flood disturbance indices in Regions A and E, respectively, where I a can express the immobility of gravels and lack of damage to trees and I e can express the mobility of large-size gravel and the wash-out condition of vegetation. The indices I a and I e may describe a medium-class disturbance to the habitat on gravel islands in the middle of a river.