Coastal zones are particularly vulnerable to climate change effects. Over the last century, sea level rose on average by 10a??12 cm per decade and did so at much higher rates in some coastal areas due to land subsidence. The 4th IPCC report highlights the increased vulnerability of the coastal zones around the world due to sea level rises in 21st Century. Key concerns due to sea level rise include flooding and salinisation and its implications for water resources. Rising sea level increases the salinity of both surface water and ground water through salt water intrusion. It is important to determine the impacts of sea level rise on salinity to devise suitable adaptation and mitigation measures and reduce impacts of salinity intrusion in coastal cities. The paper presents the outcomes of a study conducted in the coastal area of Gorai river network in the South West region of Bangladesh for developing a comprehensive understanding of the possible effects of sea level rise with the aid of a hydrodynamic model. A newly developed salinity flux model has been integrated with an existing hydrodynamic model in order to simulate flood and salinity in the complex waterways in the coastal zone of Gorai river basin. The integrated model has been calibrated and validated by numerous comparisons with measurements (tide, salinity). The model has been applied for future scenarios with sea level rise and the results obtained indicate the risk and changes in salinity. Due to sea level rise, the salinity has increased in the river and salinity intrusion length has also increased. Sea level rise of 59 cm produced a change of 0.9 ppt at a distance of 80 km upstream of river mouth, corresponding to a climatic effect of 1.5 ppt per meter sea level rise.