We present 12 seasonally resolved δ18O profiles of giant clams (Tridacna sp.) from the Huon Peninsula, Papua New Guinea, spanning discrete periods of time (9–38 years) over the past 60 ka. The interannual anomaly time series of these shells are used to reconstruct interannual variability which can predominantly be attributed in the modern climate to the El Niño–Southern Oscillation (ENSO) in this region. We have found a significant reduction in interannual δ18O variance during the early Holocene, whereas during Marine Isotope Stage 3 there were at least some periods with variance not significantly different to the twentieth century. We show that ENSO variability seen during the late twentieth century is rare but not unprecedented within glacial climates.