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In December 1991, 30 conductivity-temperature-depth (CTD) stations to 1000 dbar were obtained from the R/V Baruna Jaya I in the Flores Sea, Banda Sea, and Alor-Wetar passage of the Indonesian sea. A salinity maximum within the interval 100–150 dbar and a salinity minimum within the interval 300–350 dbar mark water mass core layers derived from the North Pacific. They are drawn into the Flores Sea from the Makassar Strait, with subsequent flow into the Banda Sea, and are weakened en route by strong vertical mixing characteristic of the Indonesian seas. In the Flores Sea, water below 300 dbar becomes saltier with increased distance from the Makassar Strait, suggesting that an advective process may be drawing relatively salty water into the Flores Sea lower thermocline from the Banda Sea. The Banda-to-Flores Sea flow may be a consequence of vertical transfer of horizontal momentum produced by the same turbulent processes that are responsible for enhanced vertical mixing. The interocean transport profile may not correspond exactly with the Pacific-to-Indian Ocean pressure gradient profile, as deeper water is carried along with the through flow by the effects of eddy viscosity. The 550-m sill at the southern end of the Makassar Strait creates a situation where downward flux of momentum entrains deeper water that must be compensated by lower thermocline water drawn from the Banda Sea. Geostrophic transport relative to 1000 dbar in the Banda Sea shows not only a strong through flow transport in the upper 300 dbar (6.3×106 m3 s−1) but also a deeper flow toward the Flores Sea (1.5×106 m3 s−1 from 300 to 500 dbar and an additional 2.4×106 m3 s−1 from 500 to 1000 dbar). A simple model suggests that the magnitude of the deeper westward flow is proportional to the vertical eddy viscosity coefficient. Water mass analysis shows that either the South Pacific or Indian Ocean can provide the lower thermocline Banda Sea water.