Salinity intrusion into estuaries depends strongly on the morphologic, topographic, hydrodynamic and tidal characteristics of estuaries. Combinations of these factors determine the flow patterns and mixing mechanisms in estuaries. Since the salinity affects water quality in estuaries, salinity intrusion length can be considered as a key parameter for estuarine management. Hence, many investigations have been conducted to predict this parameter. On the other hand, man-made modifications affect the salinity intrusion in estuaries and therefore their desirable and undesirable effects must be evaluated in advance. The aim of this study is to derive an equation to predict the influence of man-made modifications on the salinity intrusion length in estuaries. To achieve this aim, a scaling was performed on the governing equations of the salinity intrusion and a functional relationship among the salinity intrusion governing dimensionless parameters was obtained. Then an alluvial estuary was studied through a numerical model as an example. Finally, a new general empirical formula is presented to predict the salinity intrusion as a function of parameters involved mostly in estuarine modification projects.