The expendable bathythermograph (XBT) line Fremantle-Sunda Strait transects the eastern Indian Ocean between northwestern Australia and Java. It was established in 1983 with low-density sampling and upgraded to a frequently repeated line (>18 times per year) in 1987 to monitor currents. The observations during 1983 to 1994 are described and related to the field of wind stress. Variation of thermal structure shows a rich mixture of annual, semiannual, and interannual timescales. Empirical orthogonal function (EOF) analysis of anomalies of sea surface temperature (SST), dynamic height, and depth of the 20 ¿C isotherm D20 identifies two distinctive signals. The El Ni¿o-Southern Oscillation (ENSO) signal (EOF 1) appears throughout the region and is strongest off the coast of Australia. A modulation of the annual signal (EOF 2) appears off the coast of Java. EOF 2 has a shorter timescale than the ENSO signal, and its temporal coefficients are correlated to zonal winds over the equatorial Indian Ocean. For both EOFs, anomalously low SST and dynamic height occur at the same time as anomalously shallow D20 and vice versa for opposite anomalies. The XBT data are used with a climatological temperature-salinity relationship to calculate net, relative (0/400 dbar) geostrophic transports T through the section. For long timescales, T is representative of Indonesian throughflow. The variations associated with ENSO show a maximum during the La Ni¿a of 1988--1989 and minima during the El Ni¿os of 1986--1987 and 1991--1994. The peak-to-trough amplitude of the ENSO signal is 5 Sv. The ENSO signal in throughflow is discussed in terms of earlier studies. For the shorter timescales, T is representative of currents from the Indian Ocean flowing in and out of the region between northwestern Australia and Indonesia, changing the volume of upper layer water stored there. Associated with EOF 2, a sharp peak in westward transport developed during May to October 1994. ¿ American Geophysical Union 1996