Description: Based on a joint analysis of an ensemble mean of satellite sea surface salinity retrievals and the output of a high-resolution numerical ocean circulation simulation, physical processes are identified that control seasonal variations of mixed layer salinity (MLS) in the Indian Ocean, a basin where salinity changes dominate changes in density. In the northern and near-equatorial Indian Ocean, annual salinity changes are mainly driven by respective changes of the horizontal advection. South of the equatorial region, between 45°E and 90°E, where evaporation minus precipitation has a strong seasonal cycle, surface freshwater fluxes control the seasonal MLS changes. The influence of entrainment on the salinity variance is enhanced in mid-ocean upwelling regions, but remains small. The model and observational results reveal that vertical diffusion plays a major role in precipitation and river runoff dominated regions balancing the surface freshwater flux. Vertical diffusion is important as well in regions where the advection of low salinity leads to strong gradients across the mixed layer base. There, vertical diffusion explains a large percentage of annual MLS variance. The simulation further reveals that 1) high-frequency small-scale eddy processes primarily determine the salinity tendency in coastal regions (in particular in the Bay of Bengal), and 2) shear horizontal advection, brought about by changes in the vertical structure of the mixed layer, acts against mean horizontal advection in the equatorial salinity frontal regions. Observing those latter features with the existing observational components remains a future challenge.