The Yangtze and Yellow Rivers significantly influence sediment dynamics along China's continental margin through their substantial discharges and subsequent marine redistribution. However, a comprehensive understanding of coastal sedimentary responses to such mega-river-driven redistribution remains limited. This study addresses this gap by examining Holocene source-to-sink processes in Hangzhou Bay (Qiantang River estuary), a key depocenter located south of the Yangtze/Yellow estuaries, which received substantial sediment during post-glacial transgression. Geochemical fingerprinting reveals a striking compositional similarity between Holocene palaeo-valley fills in Hangzhou Bay and Yangtze deposits, identifying the Yangtze as the dominant sediment source. Unlike the Yangtze palaeo-valley—which records Yellow River influence during its 9.5–7.0 cal. ka BP southward avulsion—Hangzhou Bay clays show no detectable Yellow River signal. This contrast is attributed to: (1) sediment trapping by the deep Yangtze palaeo-valley, which inhibited southward clay transport, and (2) landward shelf clay transport driven by strong marine forces during rapid sea-level rise. Although the Yangtze remained the primary source for Hangzhou Bay, its contribution declined during 6.0–2.0 cal. ka BP. This reduction in Yangtze estuarine sediment flux correlates stratigraphically with the decay of the East Asian Summer Monsoon. Concurrent delta progradation enhanced sediment retention within the Yangtze estuary, collectively suppressing southward transfer to adjacent coasts. By elucidating Holocene sediment pathways in Hangzhou Bay and their linkages to Yangtze/Yellow estuarine dynamics, this study provides new global insights into impacts of mega-river reorganization on distal coastal sedimentary systems, particularly under changing climatic and sea-level regimes.