Like the paleo-Sutlej River, the paleo-Yamuna River has been hypothesized as a major tributary of the mighty Ghaggar-Hakra (Vedic Saraswati) River and its eastward migration to the modern Yamuna course linked to the deurbanization of the Harappan (Indus) Civilization that peaked ~4.0–3.9 thousand years before present (ka). Here we provide detrital Sr and Nd isotope variabilities in two ~48 m and one ~20 m deep cores drilled on the postulated paleochannel of Yamuna (Y2) and modern-day Yamuna bank, respectively, in the NW Indo-Gangetic Plain. Our isotopic records (87Sr/86Sr: 0.7358–0.7925, εNd: −14.6 to −21.2) suggest that these sediments were deposited at least since ~88 ka by the west-flowing paleo-Yamuna River, which migrated eastward to its current path shortly after ~18 ka. Therefore, no major fluvial activity was prevalent along the paleo-Yamuna channels during the Early and Mature Harappan phases (5.7–3.9 ka), questioning the widely popular river-culture hypothesis. However, the availability of sufficient water in the relict paleochannels due to intense Indian summer monsoon (ISM) precipitation during the early to middle Holocene, along with a stable landscape not prone to devastating floods because of the migration of paleo-Yamuna to its current course, might have helped the Harappan Civilization to flourish, and subsequently, the pronounced weakening of the ISM might have caused the demise of the Harappan Civilization.