The salinity and dissolved oxygen of water masses in the Indonesian Seas, from historical hydrographic data, are examined on isopycnal surfaces. We focus primarily on the Banda Sea, from which the bulk of the throughflow transport flows into the Indian Ocean. Dissolved oxygen proves to be a problematic conservative tracer in this region due to biological consumption in the upwelling regime of the Arafura Sea and the subsequent spreading of relatively low oxygen water over a broad area. The remaining analysis is thus restricted to salinity. We first consider a hypothesis of simple isopycnal advection and mixing between North and South Pacific low-latitude western boundary current sources. Three regimes are apparent. The surface and upper thermocline layers, down to 25.8σθ, are too fresh to fit the hypothesis. Vertical mixing of surface precipitation and runoff excesses down into the water column must be invoked. Vertical mixing is also apparent on deeper isopycnals, below 27.0σθ, where a contribution from the deep Indian Ocean can be discerned. In between, in the lower thermocline, the θ-S data are consistent with the hypothesis of purely isopycnal spreading, given a simple variation in the ratio of sources toward increasing South Pacific contribution with depth. In this regime the juxtaposition of sources leads to relatively strong gradients in water mass properties across the Banda Sea. This gradient translates into a difference in outflow characteristics between Timor and Ombai Straits, which appear to draw their waters, respectively, from the eastern and western Banda Sea. We then consider how the presence of vertical mixing modifies our inferred water mass ratio under a variety of boundary conditions. Vertical mixing effects are particularly important in the upper thermocline. In the Banda Sea, on all isopycnals down to σθ = 26.5, an increase in the degree of vertical mixing tends to decrease the relative importance of the North Pacific source. The sensitivity of the water mass ratio to degree of vertical mixing decreases with depth, and the tendency is reversed below 26.5σθ. In the Banda Sea, for plausible values of throughflow residence time and vertical diffusivity (λ = (κt)1/2 < 100 m), the North Pacific contributes 80–90% of the water mass at 26σθ, 50–60% at 26.5σθ, and only 10–30% at 27σθ. This large South Pacific contribution in the lower thermocline is supported by other studies.