In order to quantitatively estimate the volume and property transports between the South China Sea and Indonesian Seas via the Karimata Strait, two trawl-resistant bottom mounts, with ADCPs embedded, were deployed in the strait to measure the velocity profile as part of the South China Sea-Indonesian Seas transport/exchange (SITE) program. A pair of surface and bottom acoustic modems was employed to transfer the measured velocity without recovering the mooring. The advantage and problems of the instruments in this field work are reported and discussed. The field observations confirm the existence of the South China Sea branch of Indonesian throughflow via the Karimata Strait with a stronger southward flow in boreal winter and weaker southward bottom flow in boreal summer, beneath the upper layer northward (reversal) flow. The estimate of the averaged volume, heat and freshwater transports from December 2007 to March 2008 (winter) is (-2.7 ± 1.1) × 10 6 m3/s, (-0.30 ± 0.11) PW, (-0.18 ± 0.07) × 106m3/s and from May to September 2008 (summer) is (1.2 ± 0.6) × 106m3/s, (0.14 ± 0.03) PW, (0.12 ± 0.04) × 106m3/s and for the entire record from December 2007 to October 2008 is (-0.5 ± 1.9) × 10 6 m3/s, (-0.05 ± 0.22) PW, (-0.01 ± 0.15) × 106m3/s (negative/positive represents southward/northward transport), respectively. The existence of southward bottom flow in boreal summer implies that the downward sea surface slope from north to south as found by Fang et al. (2010) for winter is a year-round phenomenon. In order to quantitatively estimate the volume and property transports between the South China Sea and Indonesian Seas via the Karimata Strait, two trawl-resistant bottom mounts, with ADCPs embedded, were deployed in the strait to measure the velocity profile as part of the South China A pair of surface and bottom acoustic modems was employed to transfer the measured velocity without recovering the mooring. The advantage and problems of the instruments in this field work are reported and discussed. The field observations confirm the existence of the South China Sea branch of Indonesian throughflow via the Karimata Strait with a stronger southward flow in boreal winter and weaker southward bottom flow in boreal summer, beneath the upper layer northward (reversal) flow. The estimate of the averaged volume , heat and freshwater transports from December 2007 to March 2008 (winter) is (-2.7 ± 1.1) × 10 6 m3 / s, (-0.30 ± 0.11) PW, (-0.1 8 ± 0.07) × 106m3 / s and from May to September 2008 (summer) is (1.2 ± 0.6) × 106m3 / s, (0.14 ± 0.03) PW, (0.12 ± 0.04) × 106m3 / s and for the entire record from From January 2007 to October 2008 is (-0.5 ± 1.9) × 10 6 m3 / s, (-0.05 ± 0.22) PW, (-0.01 ± 0.15) × 106m3 / s (negative / positive represents southward / northward transport), respectively. The existence of southward bottom flow in boreal summer implies that the downward sea surface slope from north to south as found by Fang et al. (2010) for winter is a year-round phenomenon.