So far, large uncertainties of the Indonesian throughflow (ITF) reside in the eastern Indonesian seas, such as the Maluku Sea and the Halmahera Sea. In this study, the water sources of the Maluku Sea and the Halmahera Sea are diagnosed at seasonal and interannual timescales and at different vertical layers, using the state-of-the-art simulations of the Ocean General Circulation Model (OGCM) for Earth Simulator (OFES). Asian monsoon leaves clear seasonal footprints on the eastern Indonesian seas. Consequently, the subsurface waters (around 24.5σθ and at ~150 m) in both the Maluku Sea and the Halmahera Sea stem from the South Pacific (SP) during winter monsoon, but during summer monsoon the Maluku Sea is from the North Pacific (NP), and the Halmahera Sea is a mixture of waters originating from the NP and the SP. The monsoon impact decreases with depth, so that in the Maluku Sea, the intermediate water (around 26.8σθ and at ~480 m) is always from the northern Banda Sea and the Halmahera Sea water is mainly from the SP in winter and the Banda Sea in summer. The deep waters (around 27.2σθ and at ~1 040 m) in both seas are from the SP, with weak seasonal variability. At the interannual timescale, the subsurface water in the Maluku Sea originates from the NP/SP during El Nino/La Nina, while the subsurface water in the Halmahera Sea always originates from the SP. Similar to the seasonal variability, the intermediate water in Maluku Sea mainly comes from the Banda Sea and the Halmahera Sea always originates from the SP. The deep waters in both seas are from the SP. Our findings are helpful for drawing a comprehensive picture of the water properties in the Indonesian seas and will contribute to a better understanding of the ocean-atmosphere interaction over the maritime continent.