This study examined the relationship between El Niño–Southern Oscillation (ENSO) and atmospheric water isotopes during the wet season over the Maritime Continent. The model data used were obtained by incorporating stable isotopes into atmospheric general circulation and analytical moisture transport models. These models were used to analyze the climatological variables and rainout processes from various water sources that control isotopic variation. The correlation between the simulated stable isotope ratios and ENSO varied between −0.31 and 0.75 with stronger correlation over most of the Maritime Continent (|r| > 0.36, corresponding to the 95 % significance level) except Java. In general, during La Niña years, the isotopic ratio in water vapor and precipitation is smaller than that during El Niño years by approximately 2 ‰. It was suggested that anomalous water vapor flux, precipitable water, and precipitation, but not evaporation, are responsible for isotopic variation. Furthermore, it was revealed that water vapor flux is convergent (divergent) during La Niña (El Niño) years, which suggests that the strengthened (weakened) Walker Circulation increases (reduces) precipitation, resulting in lighter (heavier) atmospheric water isotopes. The relationship between isotopes and precipitation, or the so-called “amount effect”, is evident over most of the Maritime Continent. Analysis of moisture transport suggested that rainout processes control isotopic variation. An increase in the quantity of water source, expressed in precipitable water, transported from the north and south Maritime Continent during El Niño years, does not result in isotopic depletion attributable to the lack of condensation processes. Moreover, a decrease in the quantity of both water source during La Niña years does not result in isotopic enrichment attributable to intensive rainout. An asymmetric ENSO feature was found in this study, evidenced by the similar contributions of water source from the northern Maritime Continent and the Pacific Ocean during both ENSO phases.