Drying across much of the Indo-Pacific Warm Pool (IPWP) during the Last Glacial Maximum (LGM) has been widely recognized from interpretations of sedimentological, geochemical, and paleoecological records. Reconstructions of precipitation isotopic compositions have emerged as a powerful tool to reconstruct rainfall amount in many tropical regions, yet it has proven difficult to reconcile precipitation isotope records from the IPWP with records of widespread drying. To evaluate the signals preserved in precipitation isotope records, we produced new hydrogen and carbon isotope records from Lake Towuti and Lake Matano in Sulawesi, Indonesia using long-chain n-alkanes. We then compared these new records to existing n-alkanoic acid records from the same lakes and compiled available marine runoff, salinity, leaf wax hydrogen isotope (δ2Hwax), and leaf wax carbon isotope (δ13Cwax) records in the IPWP. During the last deglaciation, marine runoff and salinity proxies reveal that precipitation amount began to increase dramatically between ∼12.3 ka at the end of the Younger Dryas. A principal component analysis of precipitation isotope records indicates a shift from more 2H-enriched to 2H-depleted waxes at ∼12.3 ka as sea level rise inundates most of the Sunda and Sahul shelves, coincident with runoff and salinity proxies, suggesting precipitation isotopes respond strongly to rainfall amount in this region. Over 70% of IPWP δ13Cwax records show a transition from more to less 13C-enriched waxes beginning about 19.9 ka, prior to the reconstructed increases in precipitation. We suggest that vegetation shifted in response to the changing seasonality of precipitation. The dramatic changes in the IPWP during the last deglaciation highlight the capacity for the region to experience dynamic changes in precipitation, vegetation, and atmospheric circulation.