Nusantara, the Indonesia’s New Capital City, experienced a rare extreme rainfall event on 27 to 28 August 2021. This unusual heavy rainfall occurred during the dry season and caused severe flooding and landslides. To better understand the underlying mechanisms for such extreme precipitation events, we investigated the moisture sources and transport processes using the Lagrangian model HYSPLIT. Our findings revealed that moisture was mostly transported to Nusantara along three major routes, namely from Borneo Island (BRN, 53.73%), the Banda Sea, and its Surroundings (BSS, 32.03%), and Sulawesi Island (SUL, 9.05%). Overall, BRN and SUL acted as the main sources of terrestrial moisture, while the BSS was the main oceanic moisture origin having a lower contribution than that of its terrestrial counterpart. The terrestrial moisture transport from BRN was mainly driven by the large-scale high vortex flow, while the moisture transport from the SUL was driven by the circulations induced by boreal summer intraseasonal oscillation (BSISO) and low-frequency variability associated with La Niña. The near-surface oceanic moisture transport from BSS is mainly associated with prevailing winds due to the Australian Monsoon system. These insights into moisture sources and pathways can potentially improve skill in predictions of summer precipitation extremes in Indonesia’s New Capital City, Nusantara, and benefit natural resource managers in the region.