Excessive salinity can harm ecosystems and compromise the various anthropogenic activities that take place in river deltas. The issue of salinization is expected to exacerbate due to natural and/or anthropogenic climate change. Water regulations are required to secure a sufficient water supply in conditions of limited water volume availability. Research is ongoing in seek of the optimum flow distribution establishing longer-lasting and fresher conditions in deltas. In this study a three–dimensional (3D) numerical model was used to unravel the influence of hydrographs shape on the deltas salinity. Our results show that it is possible to improve the freshwater conditions in deltas without seeking for additional water resources but by modifying the water distribution. The peak flow magnitude and timing and the tails of a hydrograph were found to be important parameters affecting stratification, freshwater residence and renewal times. Hydrographs having lighter tails and smaller range were the most successful in keeping the delta and its river inlet fresher for longer periods. Salinity distributions showed a slower response to decreasing rather than increasing river discharges. An increase in the flow rate can achieve a desired salinity standard in much shorter time. Hydrographs with heavier tails can push the salt intrusion limit further away and are more efficient in mixing the water column. However, they present low freshwater residence and high water renewal times. These results have implications for coastal scientists and stakeholders dealing with the management of freshwater resources in river deltas across the world.