Salinity in estuaries is influenced by a variety of processes including tidal advection and diffusion and river discharge. The effect of hydrodynamic features on salinity was studied in the Senegal River Estuary (SRE). This estuary is of strategic importance for large populations, but it has been greatly affected by human action (regulation of the freshwater inflow, change in the location of the river mouth ...), which has caused major changes in salinity and ecological functioning. To analyse the impacts of these changes and to determine the spatial and temporal variations in salinity in the SRE, we used a combination of three-dimensional modelling and field measurements. The overall salinity depends on freshwater inflow and tidal fluctuations. Salinity variation is mainly driven by ebb and flood near the mouth and by fortnightly cycles upstream. The enlargement of the mouth increases salinity, whereas its shifting location changes the location of the salinity front and creates a slack water zone downstream. Connection and disconnection of the tributaries also affects the salinity. The present study explains how the recent modifications have increased spatial variation and reduced seasonal differences of salinity and provides a tool for managing the water in the estuary.