Little is known about climate changes on Flores that influenced Homo floresiensis during the period of occupation of Liang Bua (95–12 ka) or the late-surviving pygmy Stegodon lineage; both species became locally extinct at ca. 12 ka. Previous palaeoclimate analysis in this region has established that a prolonged dry period (ca. 45–12 ka) was followed by a rapid increase in rainfall, but lacks a firm chronology. Here we report initial results for stalagmites from western Flores and eastern Java. Using δ18O data from contemporaneous records, a series of isotopic shifts has been identified that reflects changes in the amount of rainfall, and in moisture sources. The isotopic signals from oxygen and carbon suggest differing ages for the rapid increase in rainfall, at ca. 13 ka and 17–16.5 ka, respectively. Thus, it cannot be determined from this evidence whether the abrupt disappearance of Stegodon and Homo floresiensis in western Flores was coincident with a major change in climate, or was caused instead, or as well, by a volcanic eruption at ca. 12 ka, or was related to the arrival of Homo sapiens at Liang Bua by ca. 10.5 ka.