Property structure and variability of the Indonesian Throughflow Water in the major outflow straits (Lombok, Ombai and Timor) are revised from newly available data sets and output from a numerical model. Emphasis is put on the upper layers of the Indonesian Throughflow that impacts the heat and freshwater fluxes of the South Equatorial Current in the Indian Ocean. During the April–June monsoon transition the salinity maximum signature of the North Pacific thermocline water is strongly attenuated. This freshening of the thermocline layer is more intense in Ombai and is related to the supply of fresh near-surface Java Sea water that is drawn eastward by surface monsoon currents and subject to strong diapycnal mixing. The freshwater exits to the Indian Ocean first through Lombok Strait and later through Ombai and Timor, with an advective phase lag of between one and five months. Because of these phase lags, the fresher surface and thermocline water is found in the southeast Indian Ocean from the beginning of the monsoon transition period in April through until the end of the southeast monsoon in September, a much longer time period than previously estimated.