This study investigates the Mindoro Strait and Sibutu Passage transports using remotely-sensed sea surface height (SSH) and ocean-bottom-pressure (OBP) data. The analysis reveals the existence of a persistent baroclinic pressure gradient that drives a deepwater overflow from the South China Sea into the Sulu Sea. The application of hydraulic theory combined with the “geostrophic control” formula yields a mean transport estimate of about 2.4 Sv (1 Sv = 106 m3 s−1) through the Mindoro Strait and about 2.8 Sv through the Sibutu Passage. Most of this water enters the Sulu Sea through the bottom layer of the Mindoro Strait and exits the Sulu Sea in the upper layer of the Sibutu Passage. The analysis also provides the first satellite-based observational evidence on the seasonal and interannual variation of the Mindoro Strait and Sibutu Passage transports for the period from January 2004 to December 2007.