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A riffle-pool structure is a representative physical structure of bed in rivers. The change in the physical parameter of the habitat could lead to changes in the sound environment of rivers, which are expressed by underwater acoustics. This change in underwater sound affects fish habitat. In this study, the changes of underwater acoustics were analyzed according to the change of pool-riffle sequence in a natural river. And the correlation between underwater acoustics and hydraulic characteristics was investigated. The survey for underwater acoustics was performed in the Namdae stream where is in Gangwon province. This stream belongs to the Han River basin and the river length is 39.01 km and the catchment area is 127.56 km2. The Namdae stream is a river that accounts for more than 70% of salmon returning to South Korea. The spawning salmon will return to this area around November after growing in the Bering Sea. It is important to manage the fish habitat in this river so there is a lot of research on the enhancement of fish habitat. Hydraulic characteristics were changed by the river bed structure. In this study, we investigated the relationship between underwater acoustic characteristics and hydraulic factors such as riverbed material, flow rate and water depth of each habitat type at 12 sites. The characteristics of underwater acoustic differed relative to different hydraulic factors of the two habitats, which is riffle and pool. The sound pressure level of riffles was relatively higher than that of the pools due to bed materials, shallow depth and high water velocity of riffles. In the future, it is considered that the underwater sound can be utilized as a parameter to evaluate the physical habitat environment of the river.