Ecological evaluation of riverbed geomorphology is essential for environmental assessment of river works as well as for establishment of target images in river management planning. In this paper, we analyzed inter-relationships between the reach-scale channel configuration (RSCC) and habitat structure on the riverbed based on the historical changes of riverbed geomorphology on the Kizu River in Japan. The analyses used nine sets of aerial photographs taken from 1948 to 2012, which resulted in a total of eight RSCC types classified as Single Sinuous, Semi-Wandering-Straight, S-W-Sinuous, Wandering-Straight, W-Sinuous, Bifurcated-Straight, B-Sinuous, and Braided Sinuous. Aquatic habitats were classified into four lotic habitats (Main Slow, Secondary Slow, Gently Bending Riffle, and Sharply Bending Riffle) and four lentic habitats (Bar-Head Wando, Bar-Tail Wando, Active Pond, and Terrace Pond), and their richness and diversity indices were analyzed in relation to RSCC types. The results showed that Braided Sinuous channels had the maximum number of habitats, and Wandering-Straight and Bifurcated-Sinuous channels showed higher habitat diversity than the others. These results indicated that the target image of the Kizu River management will be Braided-Sinuous channels in terms of habitat abundance, whereas they will be Wandering-Straight and Bifurcated-Sinuous channels from the aspect of habitat diversity.