The hydrologic response to climate forcing in the Indo-Pacific warm pool region has varied spatially over the past 25,000 years. For example, drier conditions are inferred on Java and Borneo for the period following the end of the Last Glacial Maximum, whereas wetter conditions are reconstructed for northwest Australia. The response of vegetation to these past rainfall variations is poorly constrained. Using a suite of 30 surface marine sediment samples from throughout the Indo-Pacific warm pool, we demonstrate that today the stable isotopic composition of vascular plant fatty acids (13 Cfa) reflects the regional vegetation composition. This in turn is controlled by the seasonality of rainfall consistent with dry season water stress. Applying this proxy in a sediment core from offshore northeast Borneo, we show broadly similar vegetation cover during the Last Glacial Maximum and the Holocene, suggesting that, despite generally drier glacial conditions, there was no pronounced dry season. In contrast, 13Cfa and pollen data from a core off the coast of Sumba indicate an expansion of C 4 herbs during the most recent glaciation, implying enhanced aridity and water stress during the dry season. Holocene vegetation trends are also consistent with a response to dry season water stress. We therefore conclude that vegetation in tropical monsoon regions is susceptible to increases in water stress arising from an enhanced seasonality of rainfall, as has occurred in past decades. © 2014 Macmillan Publishers Limited.