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Acoustic Doppler current profiler observations were carried out at two stations along a transect northwest of the Karimata Strait from December 2007 to November 2008. One month and 10 months of full‐depth current data were obtained at the western and eastern stations, respectively. The observations show that the South China Sea (SCS) water flows persistently to the Indonesian seas (ISs) in boreal winter. On the basis of current, temperature, and salinity observations by conductivity‐temperature‐depth casts and bottom‐mounted sensors, the volume, heat, and freshwater transport from the SCS to ISs in the month from 13 January to 12 February 2008 are estimated to be 3.6 ± 0.8 Sv (Sv = 106 m3/s), 0.36 ± 0.08 PW, and 0.14 ± 0.04 Sv, respectively. The corresponding transport‐weighted temperature is 27.99°C. A downward sea surface slope from north to south at the study area in boreal winter is also found. The observations confirm the existence of the SCS branch of the Pacific‐to‐Indian‐Ocean throughflow in boreal winter and the reversal of the Karimata Strait transport in boreal summer. The seasonal variability in the Karimata Strait transport can exceed 5 Sv. It is proposed that the Karimata Strait throughflow plays a double role in the total Indonesian Throughflow transport, which is especially evident in boreal winter. The negative effect of the double role is reducing the Makassar Strait volume and heat transports; the positive effect is that the Karimata Strait throughflow itself can contribute volume and heat transports to the total Indonesian Throughflow.