This paper investigates mechanisms controlling the mixed-layer salinity (MLS) in the tropical Pacific during 1990–2009. We use monthly 1° × 1° gridded observations of salinity, horizontal current and fresh water flux, and a validated ocean general circulation model with no direct MLS relaxation in both its full resolution (0.25° and 5 days) and re-sampled as the observation time/space grid resolution. The present study shows that the mean spatial distribution of MLS results from a subtle balance between surface forcing (E − P, evaporation minus precipitation), horizontal advection (at low and high frequencies) and subsurface forcing (entrainment and mixing), all terms being of analogous importance. Large-scale seasonal MLS variability is found mainly in the Intertropical and South Pacific Convergence Zones due to changes in their meridional location (and related heavy P), in the North Equatorial Counter Currents, and partly in the subsurface forcing. Maximum interannual variability is found in the western Pacific warm pool and in both convergence zones, in relation to El Niño Southern Oscillation (ENSO) events. In the equatorial band, this later variability is due chiefly to the horizontal advection of low salinity waters from the western to the central-eastern basin during El Niño (and vice versa during La Niña), with contrasted evolution for the Eastern and Central Pacific ENSO types. Our findings reveal that all terms of the MLS equation, including high-frequency (<1 month) salinity advection, have to be considered to close the salinity budget, ruling out the use of MLS (or sea surface salinity) only to directly infer the mean, seasonal and/or interannual fresh water fluxes.