Water level management strategies specify that the impoundment of the Three Gorges Reservoir (TGR) starts from 145m asl in September to 175m asl in November. The water level is maintained for three months and then returned to 145m asl again in May. Consequently, three types of water-level-fluctuation zones appear along the Three Gorges Reservoir tributaries banks:(1) The area from the estuary to the 145-m backwater (completely-flooding reach), where the former natural riparian zone is submerged permanently since its elevation is below 145m asl; (2) the 145-m backwater area to the 175-m backwater area (double-flooding reach), which is affected by summer flooding from July to September as well as by impoundment from September to May; (3) the area above the 175-m backwater area (natural reach), which is not affected by reservoir water storage. In order to distinguish the influence of reservoir water storage on habitat factors in the different river reaches, we investigated the river habitats of 254 reaches in 36 major tributaries in the Three Gorges Reservoir area. Based on the results of these investigations, we used factor analysis to assess the 18 indicators on river hydrology, river morphology, and the water-level fluctuation zone habitat of different river habitats, and analyzed the relationship between the degree of flow regime naturalness and habitat factors in different reaches. The results showed that vegetation conditions are important habitat factors in three different types of sections. Affected by the impoundment of the Three Gorges reservoir, most riparian vegetation is herbaceous and flooding-tolerant, with nearly no trees or shrubs. Compared with the double reach and natural reach zones, the completely reach zone was subject to significant changes in the flow pattern, surface coverage, width of the buffer zone, and wetting rate. The effects of flow regime conditions on habitat factors in different river reaches differed.