AbstractMechanisms of salinity anomalies associated with the positive Indian Ocean Dipole (pIOD) are investigated through a series of sensitivity experiments and an online budget analysis using a regional ocean model. Special emphasis is placed on the contribution from the rectified effects due to high‐frequency variability, which was not quantitatively discussed in previous studies. The results from sensitivity experiments show that positive sea surface salinity (SSS) anomalies in the southeastern tropical Indian Ocean are primarily caused by reduction in precipitation and partly by enhanced evaporation due to increased wind speed, while negative SSS anomalies in the central‐eastern equatorial Indian Ocean are generated by zonal advection anomalies induced by anomalous wind stress, consistent with previous studies. Completely new results are that the modulation of nonlinear salinity advection associated with mesoscale eddies also plays an important role in determining the spatial pattern of SSS anomalies, especially in the southeastern tropical Indian Ocean. On the other hand, subsurface salinity anomalies are almost entirely caused by wind stress effects mediated by ocean dynamical processes. Further decomposition of advective anomalies suggests that they are mainly explained by the pIOD‐related current anomalies governed by equatorial wave dynamics. However, a vertical shift of nonlinear freshening due to high‐frequency variability also substantially contributes to the generation of positive subsurface salinity anomalies in the eastern equatorial Indian Ocean. Our results show that large‐scale oceanic changes in response to the pIOD‐related atmospheric anomalies are the key drivers of the observed salinity anomalies, while some nonlinear effects also seem to be at work.