For the dynamic balance of the world ocean circulation, the flow through the Indonesian archipelago needs to be quantified. Part of the Java Australia Dynamic Experiment program was to occupy hydrographic sections during the two opposite seasons. Here we present and discuss the February 1992 geostrophic estimate of the throughflow. The appearance of the east-flowing Java Current, flowing in the 80 km off the Indonesian coast, led to a net total transport of a few 106 m3 s−1 eastward, opposite to the expected sense of net transport. Uncertainty in this transport, estimated from the repeated casts, reaches 9 106 m3 s−1. This large error could be attributable to internal wave motions. Estimates of the transport from the conductivity-temperature-depth data and from the temperature profile associated to the Levitus  data set have been compared. Comparison with August 1989 results shows that the main westward current, corresponding to the South Equatorial Current, is located north of the hydrological front in both seasons. The largest transport variation between the two cruises is located along the Indonesian coast, with the reversal of the Java Current. The mesoscale current variability is enhanced in the southern part of the section in February 1992. These transport evaluations, made in the two opposite seasons and in two different years, 18 ± 7 106 m3 s−1 westward in August 1989 and 2.6 ± 9 106 m3 s−1 eastward in February 1992, give an extreme range of the net throughflow.