Climate‐coupled models typically overestimate the amplitude of the seasonal cycle of sea surface salinity (SSS) in the tropics. A better understanding of the mechanisms controlling the seasonal variance of SSS could provide directions for improving the representation of the SSS seasonal cycle amplitude in these models. In this work, we use a novel framework, based on seasonal salinity variance budget (SVB), which we apply to the Estimating the Circulation and Climate of the Ocean (ECCO) state estimate, to study the mechanisms controlling the variance of seasonal SSS in the tropical oceans. Our findings reveal that oceanic advection, vertical diffusion, and freshwater fluxes from rivers and precipitation all play an important role in controlling the amplitude of the seasonal cycle, but their impact varies regionally. The SVB framework effectively distinguishes between “source” (mechanisms that enhance variance) and “sinks” (mechanisms that dampen variance). We show that vertical diffusion acts as the primary sink across most regions, except for the eastern Arabian Sea where precipitation dominates as the main sink. In other regions of the tropical oceans, precipitation and river runoff act as sources of variance. The effect of the advective term on the SSS variance is shown to be mainly the sum of two terms—first, a term associated with the spatial redistribution of the variability by the eddy‐parametrized oceanic circulation, and second, a term associated to a transfer of salinity variance between the time mean and seasonal circulations.