The objective of this paper was to describe the effect of estuarine flooding leading to estuary transverse flow salinity intrusion specifically in the Selangor River estuary. The simulation of Selangor River estuary has been carried out using a multi-dimensional hydrodynamic and transport model. The Selangor River estuary model has been calibrated and validated using data on November 2005 for water-level calibration and from May to June 2014 for salinity validation. The results of the simulation show that the salinity level decreases when the water-level increases due to high fresh water discharge from the river upstream for different return periods of 10, 50, and 100 years.