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Mooring, CTD, and ADCP observations were made in 2012 in and around the Toyama Trough (TT) cutting across a continental shelf along the Japanese coast of the Japan Sea between Noto Peninsula (NP) and Sado Island (SI) to investigate spatiotemporal characteristics of path transition of the coastal branch of the Tsushima Warm Current (CBTWC). Around SI, downstream of the TT boundary, a wavelike alongshore current perturbation, accompanied by sea level rise, was observed. This perturbation occurred after the seasonal amplification of the CBTWC around the NP on the upstream boundary of the TT. This process was delineated by the results of numerical experiments performed with a two-layer model using idealized topography. The model showed that a current path of the CBTWC shifted from alongshore mode to offshore mode bridged over the TT in association with the lee eddy development behind the NP toward the SI over the TT. This lee eddy is generated by positive vorticity induced over topographic discontinuity between the continental shelf off the northern coast of the NP and deeper region of the TT. The model indicated the period of eddy formation is 60–90 days if the volume transport is 1 Sv (1 Sv ≡ 106 m3 s−1), whereas the observations showed the formation period was only 47 days at 1.2 Sv of volume transport. To explain this discrepancy, temporal variation of the CBTWC, vortex supply from preexisting eddies, or eddies caused by the scattering of coastal-trapped waves were suggested as new processes that accelerate the growth rate of the lee eddy.