Existing paleoclimate data suggest a complex evolution of hydroclimate within the Indo-Pacific Warm Pool (IPWP) during the Holocene epoch. Here we introduce a new leaf wax isotope record from Sulawesi, Indonesia and compare proxy water isotope data with ocean-atmosphere general circulation model (OAGCM) simulations to identify mechanisms influencing Holocene IPWP hydroclimate. Modeling simulations suggest that orbital forcing causes heterogenous changes in precipitation across the IPWP on a seasonal basis that may account for the differences in time-evolution of the proxy data at respective sites. Both the proxies and simulations suggest that precipitation variability during the September–November (SON) season is important for hydroclimate in Borneo. The preëminence of the SON season suggests that a seasonally lagged relationship between the Indian monsoon and Indian Ocean Walker circulation influences IPWP hydroclimatic variability during the Holocene.