In this study, we analyse the seasonal variability of the sea surface salinity (SSS) for two coastal regions of the Gulf of Guinea from 1995 to 2006 using a high resolution model (1/12°) embedded in a Tropical Atlantic (1/4°) model. Compared with observations and climatologies, our model demonstrates a good capability to reproduce the seasonal and spatial variations of the SSS and mixed layer depth. Sensitivity experiments are carried out to assess the respective impacts of precipitations and river discharge on the spatial structure and seasonal variations of the SSS in the eastern part of the Gulf of Guinea. In the Bight of Biafra, both precipitations and river runoffs are necessary to observe permanent low SSS values but the river discharge has the strongest impact on the seasonal variations of the SSS. South of the equator, the Congo river discharge alone is sufficient to explain most of the SSS structure and its seasonal variability. However, mixed layer budgets for salinity reveal the necessity to take into account the horizontal and vertical dynamics to explain the seasonal evolution of the salinity in the mixed layer. Indeed evaporation, precipitations and runoffs represent a relatively small contribution to the budgets locally at intraseasonal to seasonal time scales. Horizontal advection always contribute to spread the low salinity coastal waters offshore and thus decrease the salinity in the eastern Gulf of Guinea. For the Bight of Biafra and the Congo plume region, the strong seasonal increase of the SSS observed from May/June to August/September, when the trade winds intensify, results from a decreasing offshore spread of freshwater associated with an intensification of the salt input from the subsurface. In the Congo plume region, the subsurface salt comes mainly from advection due to a strong upwelling but for the Bight of Biafra, entrainment and vertical mixing also play a role. The seasonal evolution of horizontal advection in the Bight of Biafra is mainly driven by eddy correlations between salinity and velocities, but it is not the case in the Congo plume.