To trace past changes in flooding frequency, we investigated fluvial sediments in the middle reach of the Nakdong River, South Korea. Sediments with larger grain size, lower total organic carbon percentage, and depleted δ13C values in the recovered sediment cores were interpreted as periods of more frequent flooding. Patterns of decreased long-term flooding frequency and vegetation changes during the early to late Holocene were similar to the decreasing regional summer monsoon intensity. Multicentennial frequent flooding periods in the study area (2900–3400 cal yr BP, 3600–3900 cal yr BP, 4600–5300 cal yr BP, and 5800–6400 cal yr BP) corresponded to stronger El Niño–Southern Oscillation (ENSO) activity periods. Based on previous studies showing that high-frequency tropical typhoon-driven coastal inundation along the western coast of Japan during the middle to late Holocene was coupled with stronger ENSO activity, it is likely that the observed centennial-to-millennial-scale flood frequency change in South Korea was influenced mainly by changes in the genesis and tracks of tropical typhoons at centennial-to-millennial time scales. This suggests that the centennial-to-millennial-scale hydrologic changes in East Asia were linked to the remote atmospheric-oceanic circulation changes represented by an ENSO-like pattern.