Accurate projections and attribution of Arctic Ocean changes in climate models require a good understanding of the mechanisms underlying interannual salinity variability in the region. Although some mechanisms have been extensively studied in idealized setting, in particular for the dynamics of the Beaufort gyre (BG), it remains unclear how applicable they are to more complex systems. This study introduces a new diagnostic based on salinity variance budget to robustly assess the mechanisms of salinity variations. The diagnostic is then applied to the “Estimating the Circulation and Climate of the Ocean” state estimate. Results indicate that the advection of salinity anomaly in the direction of the mean salinity gradient made by velocity anomalies is the primary source of interannual salinity variability. These velocities are primarily attributed to fluctuating winds via Ekman transports. Fluctuating surface freshwater fluxes from the atmosphere and sea ice are the second most important source of variability and cannot be neglected. The two sinks of interannual salinity variance are associated with the erosion of large scale gradients of the mean circulation by eddies and to a lesser extent to the diffusive terms. Over continental shelves, particularly over the East Siberian Shelf (ESS), ocean surface freshwater fluxes and diffusion play a more important role than in the deep basins. We also report a strong intensification of all sources and sinks of interannual salinity variability in the BG and an opposite weakening in the ESS in the second decade of the analysis (2004–2014) with respect to the first (1993–2003).