Flooding due to Caspian Sea level rise (CSLR) resulting from climate change may have serious ecological and socio-economic consequences. According to estimates from the Caspian Environment Programme (CEP), global warming until 2016 may cause a relative CSLR in Iranian coastal area of 20–120 cm. Rising the Caspian Sea level will not only inundate low-lying coastal regions, but it will also contribute to the redistribution of sediment along sandy coasts. In the present paper the possible impact of a CSLR of this magnitude on coastal habitat types is discussed based on topography at the Anzali Lagoon area in the North of Iran. Coastal marshes are susceptible to accelerated CSLR because their vertical accretion rates are limited and they may drown. As the Anzali Lagoon convert to the Caspian Sea, tidal exchange through inlets increases, which leads to sand sequestration on tidal deltas, erosion of adjacent barrier shorelines, and change the ecological conditions. The CSLR is expected to cause a change in groundwater level, a horizontal displacement of vegetation zones and a reduction in area, depending on accretion rate (sedimentation), local topography and inland land-use.