The benthic front in the Japan Sea has distinct potential temperature (PT) differences and is formed at the boundary between low-PT, high-oxygen Japan Basin Bottom Water (JBBW) and high-PT, low-oxygen Yamato Basin Bottom Water (YBBW). However, the YBBW originates from the JBBW. Thus, to study the transport and modification processes of these BWs in detail, shipboard observations were conducted near the benthic front in the spring of 2015 and summer of 2016. The water-mass classification of both BWs was determined using dissolved oxygen (DO)-PT diagrams and a substantial mixing between the two BWs was formed near the head of the JBBW, which entered the YB from the JB side. Thus, it can be inferred that this mixed water is transported counter-clockwise by a nearly closed horizontal circulation flow in the YB, heated by geothermal heating, consumed by oxygen, changed into vertically mixed YBBW with high-PT and low-DO, and then contacts JBBW again to form the benthic front. Detailed cross-sectional observations of the mixing zone on the YBBW side of the benthic front (with an interval of ～1 mile between stations) showed a wavy structure with a horizontal scale of ～10 km, demonstrating a transient water-mass mixing state. The most interesting feature is that the vertical distributions of PT and DO do not coincide. Although the wavy structure shown by the temperature field appears to be trapped by the sea bottom, the highly oxygenated mixed water (originating from JBBW) was located in one half ( ～5 km) of the low-PT bottom layer and the hypoxic YBBW in the other half. Therefore, the modification process caused by the mixing of both BWs indicates the involvement of bottom-trapped disturbances (internal waves or horizontal eddies) with a wavelength of ～10 km.