The Indonesian Throughflow (ITF) is thought to influence thermohaline circulation dynamics and is important for understanding global climate and the marine ecosystem. The physical and chemical properties of North Pacific Intermediate Water (NPIW) and the underlying deep water incorporated into the ITF appear to be the result of climate-related preconditioning in the North and South Pacific. Thus, these high-latitude source waters play an important role in the Indo-Pacific oceanography. Here, we present the results of down-core faunal analyses of fossil ostracods (Crustacea) that we argue reflect NPIW variability in the central part of the Makassar Strait in the ITF over the past 15 k.y. The results show that the warm-water and low-oxygen–water fauna, and species diversity, rapidly increased at ca. 12 ka, reaching maxima during the Younger Dryas (YD). We interpret the faunal change and the diversity maximum at ca. 12 ka as a response to the stagnation of intermediate water due to the decline in ITF intensity during the YD. After ca. 7 ka, the ostracod faunal composition clearly changed from a relatively shallower, warmer, and low-oxygen fauna to a relatively deeper, colder, and high-oxygen fauna. Our interpretation is that the ostracod fauna was responding to the deglacial–early Holocene sea-level rise and the ventilation variations due to the mixing of the NPIW and the underlying deep water. The intermediate-water environment and the ecosystem in the ITF could have been driven by the intensification of the influence of the underlying deep water, caused by changes in the southern high-latitude source due to the latitudinal displacements of the southwesterly winds.