Five hydrographic sections across the Indonesian throughflow from the World Ocean Circulation Experiment (WOCE) and the Java Australia Dynamic Experiment (JADE) are used to examine seasonal water mass and density distributions, including semiannual variation of the South Java Current. Altimetric sea surface height variations match dynamic height along each WOCE cruise track remarkably well. They also reveal energetic eddies and meanders of the current system south of Java with intraseasonal (60-day) changes in surface dynamic height comparable in magnitude to seasonal and interannual variations. Through the formation of discrete eddies and meanders of the large-scale zonal flows, intraseasonal fluctuations account for much of the variation in water mass structure between cruises.¿ 1997 American Geophysical Union