Intraseasonal variability and tides along the Makassar Strait, the major route of Indonesian throughflow, are investigated using spectral and time-frequency analyses which are applied to sea level, wind and mooring data. Semidiurnal and diurnal tides are dominant features, with higher (lower) semidiurnal (diurnal); energy in the north compared to the south. Sea levels and mooring data display intraseasonal variability which are probably a response to remotely forced Kelvin waves from the Indian Ocean through Lombok Strait and to Rossby waves from the Pacific Ocean. Sea levels in Tarakan and Balikpapan and Makassar mooring velocities reveal intraseasonal features with periods of 48--62 days associated with Rossby waves from the Sulawesi Sea. Kelvin wave features with periods of 67--100 days are seen in Bali (Lombok Strait), at the mooring sites and in Balikpapan, however, they are not seen in Tarakan, which implies that these waves diminish after passing through the Makassar Strait. ¿ 2000 American Geophysical Union