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The mean circulation and volume budgets in the upper 1200 m of the Maluku Sea are studied using multiyear current meter measurements of four moorings in the Maluku Channel and of one synchronous mooring in the Lifamatola Passage. The measurements show that the mean current in the depth range of 60–450 m is northward toward the Pacific Ocean with a mean transport of 2.07–2.60 Sv (1 Sv ≡ 106 m3 s−1). In the depth range of 450–1200 m, a mean western boundary current (WBC) flows southward through the western Maluku Sea and connects with the southward flow in the Lifamatola Passage. The mean currents in the central-eastern Maluku Channel are found to flow northward at this depth range, suggesting an anticlockwise western intensified gyre circulation in the middle layer of the Maluku Sea. Budget analyses suggest that the mean transport of the intermediate WBC is 1.83–2.25 Sv, which is balanced by three transports: 1) 0.62–0.93 Sv southward transport into the Seram–Banda Seas through the Lifamatola Passage, 2) 0.97–1.01 Sv returning to the western Pacific Ocean through the central-eastern Maluku Channel, and 3) a residual transport surplus, suggested to upwell to the upper layer joining the northward transport into the Pacific Ocean. The dynamics of the intermediate gyre circulation are explained by the potential vorticity (PV) integral constraint of a semienclosed basin. Significance Statement: The Indonesian Throughflow plays an important role in the global ocean circulation and climate variations. Existing studies of the Indonesian Throughflow have focused on the upper thermocline currents. Here we identify, using mooring observations, an intermediate western boundary current with the core at 800–1000-m depth in the Maluku Sea, transporting intermediate waters from the Pacific into the Seram–Banda Seas through the Lifamatola Passage. Potential vorticity balance suggests an anticlockwise gyre circulation in the intermediate Maluku Sea, which is evidenced by the mooring and model data. Transport estimates suggest northward countercurrent in the upper Maluku Sea toward the Pacific, supplied by the Lifamatola Passage transport and upwelling from the intermediate layer in the Maluku Sea. Our results suggest the importance of the intermediate Indonesian Throughflow in global ocean circulation and overturn. More extensive investigations of the Indo-Pacific intermediate ocean circulation should be conducted to improve our understanding of global ocean overturn and heat and CO2 storages. [ABSTRACT FROM AUTHOR]