Paleoclimate evidence from South America and Asia has been interpreted to indicate that tropical rainfall migrated southward during the Northern Hemisphere cooling associated with Heinrich stadial 1 (HS1), an event of massive iceberg discharge to the North Atlantic ca. 18–15 ka. Although arid conditions associated with such a shift are well documented in southern Asia, as far south as Borneo, debate still exists regarding the precipitation response in southern Indonesia and Australia during HS1. This study utilizes concentrations of the long-lived nuclide 232Th as a proxy for detrital riverine input and 230Th normalization to estimate the history of preserved fluxes reaching the seafloor in the Flores Sea, located between southern Sulawesi and the Lesser Sunda Islands, Indonesia. Because the only source of 232Th to the ocean is continental minerals, this proxy is a robust indicator of continental weathering. The 230Th normalized burial fluxes of lithogenic and biogenic matter demonstrate that both detrital and biogenic fluxes in the Flores Sea were higher during HS1 than any other period in the past 22 k.y. High detrital fluxes indicate enhanced precipitation runoff from surrounding landmasses during a period of maximum southward shift of the Intertropical Convergence Zone. This study further constrains the northern limit of enhanced rainfall associated with a southward shift of Australian monsoon-related rainfall at the time of HS1 and highlights the value of 232Th as a proxy of continental input to deep-sea sediment records.