Salinity in the Indonesian seas integrates regional oceanographic and atmospheric processes, such as Indonesian Throughflow (ITF) and monsoon rainfall. Here we present a multicentury (1777–1983) δ18O coral record from Nightcliff Reef, located in the Timor Passage off the coast of northern Australia, which we use to infer local salinity change. We show that Australian monsoon rainfall and ITF influence salinity at the study site. These reconstructed salinity changes in the Timor Passage correlate with changes in Pacific sea surface temperature (SST) modes, including the El Niño Southern Oscillation (ENSO) and the Interdecadal Pacific Oscillation (IPO). While environmental stress creates challenging conditions for coral growth, this record particularly tracks the central Pacific signature of ENSO‐driven interannual variability, in agreement with reconstructions of rainfall across northern Australia. The strength of interannual variance in the record follows fluctuations in other local ENSO‐sensitive rainfall reconstructions, demonstrating a strong regional ENSO signature. However, this regional pattern differs from variance in composite ENSO reconstructions, suggesting that the multi‐site nature of these reconstructions may create biases. Salinity variability on decadal and longer time scales occurs throughout the record. Some of these oscillations are consistent with other ITF‐sensitive coral records. Our new salinity record adds a strongly Pacific‐sensitive record to the existing suite of regional paleoclimate reconstructions. Relationships among these records highlight the complexity of salinity in the Indonesian seas and the controls on its variability.