The near closure of the Panama Seaway during the late Miocene resulted in the modification of deep-ocean currents and the formation of modern oceanic circulation. However, it is unclear how this closure impacted the north Pacific western-boundary deep circulation since the late Miocene. Here, we combine Nd isotope records in the north Pacific and a newly developed water-mass proxy (amorphous Fe hydroxide content, AFHs) from the western Pacific to investigate deep-current evolution since the late Miocene. These proxies consistently indicate a significant deep water-mass change in the north Pacific at ~5 Ma, reflecting shoaling of the Panama seaway that curtailed intermediate and deep-water exchange between the East Equator Pacific and Atlantic. Although intensification of Antarctic bottom water since ~3.4 Ma (Northern Hemisphere Glaciation) has been widely documented, a decrease in western-boundary currents has occurred since ~3 Ma. We suggest that this phenomenon is likely due to the increased mixing of south-ward and north-ward deep western-boundary currents in the north Pacific. This water mass mixing may have a significant impact on the western Pacific biogeochemical cycling.