Arvand River Estuary is the most important inland water body of Iran and its discharge has been reduced in the last decades due to construction of several dams. Hence, a two-dimensional laterally averaged time dependent hydrodynamic and water quality model called CE-QUAL-W2 was applied to this estuary to assess the impacts of river discharge reduction. The model was first implemented with three different closure schemes for parameterization of vertical transport of mass and momentum. It was found that the W2N scheme performs better than the other schemes in predicting the vertical salinity structure. The model was then used for prediction of salinity intrusion in different hydrological conditions and a simple equation was obtained for estimation of the intrusion length as a function of upstream freshwater discharge.