The seasonal variability of salinity transport in the Indian Ocean is investigated using the high-resolution global HYbrid Coordinate Ocean Model (HYCOM). Mechanisms and physical parameters that control the salinity budget are examined. Results show the influence of freshwater forcing and zonal advection as the dominant mechanisms of sea surface salinity (SSS) variability. Precipitation is highest in the eastern Bay of Bengal (BoB), where it shows seasonal variation, and in the south equatorial eastern Indian Ocean (EIO), where it was consistently high year-round. These patterns result in significant seasonal variation in the SSS in the BoB and almost no variation in the EIO. Zonal SSS transport was higher than meridional SSS transport with the strongest seasonality observed along the Sri Lankan region. Results of depth-integrated transport show northward salt transport in the bottom layers and a southward salt transport in the surface layers. The 4 year mean net flux of depth-integrated salt transport was southward (−154.8 × 106 kg/s to −552.4 × 106 kg/s) at all latitudes except at 20°N, where it was northward (396 × 106 kg/s). Transport generally increases southward with the highest transports occurring in the south (10°S–35°S) and a maximum at 30°S. Analyses of meridional Ekman volume and salt transport show a predominantly southward transport, an indication of the strong influence of SW monsoonal winds. It is anticipated that this study will be useful in computing salt transport using satellite-derived salinity data from the European Space Agency (ESA) Soil Moisture and Ocean Salinity (SMOS) and NASA Aquarius salinity missions.