Field measurements in complex estuarine systems are not always adequate to characterise the hydrodynamic behaviour of these systems and the degree to which they are affected by seawater intrusion. The model MIKE21 was used to examine the hydrodynamic regime and degree of seawater intrusion in the Shatt Al-Arab estuary under three scenarios. The model was calibrated using field measurements of vertical salinity distribution and flow that were obtained in 2013, 2014 and 2016 from a boat at six stations along the main channel. These parameters were utilised to simulate the relationship between freshwater discharge and saltwater intrusion. Results show that river flows and tidal energy are the two main factors that influence the Shatt Al-Arab estuary in terms of stratification extent and circulation pattern. Tidal range fluctuations, particularly the semidiurnal tide, are another influencing factor on the saltwater spatial patterns along the Shatt Al-Arab channel. Nowadays, seawater intrusion extends 86 km upstream from the channel mouth. Within two decades, hydrodynamic behaviour is predicted to increase salinity for more than 100 km upstream from Faw city. The modelling clarified the minimum freshwater discharge required at the Abu Flus channel measurement station to maintain an acceptable salinity level along the channel. Understanding the relationship between freshwater discharge and salinity allows informed decisions to be made regarding water usage and flows in the region for sustainable water governance that limits environmental degradation. Such an approach is applicable worldwide within similar coastal conditions.