An array of shallow pressure gauge pairs is used to determine shallow geostrophic flow relative to an unknown mean velocity in the five principal straits that separate the eastern Indian Ocean from the interior Indonesian seas (Lombok Strait, Sumba Strait, Ombai Strait, Savu/Dao Straits, and Timor Passage). Repeat transects across the straits over several tidal cycles with a 150-kHz acoustic Doppler current profiler were made during three separate years, and provide a first look at the lateral and vertical structure of the upper throughflow in these straits as well as a means of “leveling” the pressure gauge data to determine the mean shallow velocity and provide transport estimates. We estimate a total 2-year average transport for 1996–1997 through Lombok, Ombai, and Timor Straits as 8.4 ± 3.4 Sv toward the Indian Ocean. The flow structure in the upper 200 m is seen to be similar in Lombok, Sumba, and Ombai Straits, with a division into two layers, governed by different dynamics, where the upper layer episodically flows away from the Indian Ocean. Laterally, flow tends to be strongest in the deepest parts of the channel, with the exception of Lombok Strait which shows a consistent intensification of flow toward the western side. Eastward flowing northern boundary currents in Sumba and Ombai Straits suggest that the South Java Current may penetrate to the Banda Sea, farther eastward than previously documented. Although additional observations are required for a conclusive comparison, the estimated transport time series suggest differences in timing of outflow into the Indian Ocean relative to inflow from the Pacific of a size that could significantly impact the Banda Sea thermocline structure.