The mean sea level in the Bay of Biscay is expected to rise between 29 and 49 cm from 2001 to 2099, as a result of regional thermal expansion and global ice-melting. The objective of this contribution is to assess the impacts of the future projected sea level rise (SLR) in the Bay of Biscay and extreme wave events on Basque coastal habitats (saltmarshes, sandy beaches and dunes, estuaries and urban areas) by generating flood risk maps within the Basque coast (Gipuzkoan coast and the Oka estuary). A flood-risk map has been generated by delimiting the SLR projected (i.e., 49 cm) over a high-resolution Digital Elevation Model (DEM). This DTM has been extracted from airborne laser altimetry data (topographic and bathymetric LiDAR). Also, the risk of flood during storm-surge events has been calculated, by combining the action from tidal level (as the sum of the astronomic tide component and the meteorological conditions) and run-up. The impacts on land use and biological communities have been assessed, by overlaying the flood risk maps and a coastal habitat classification. The results indicate that sea level rise and extreme waves predicted with a 50-yr return period will affect 110.8 ha and 164.1 ha, respectively, of the supralittoral area of the Gipuzkoan coast by the end of the 21st century. The impacted areas by sea level rise are concentrated over low-lying areas within the inner estuaries, with terrestrial and artificial habitats being the most affected. Sandy beaches are expected to undergo mean shoreline retreats of between 25% and 40%, of their width. The Oka estuary is expected to be affected by 12 ha by the sea level rise. The extreme waves predicted with a 50-yr return period will affect mainly sandy beaches, harbours and urban areas exposed to high wave energy (NW orientation). The risk assessment of the areas, coastal land uses and habitats that will be affected is potentially useful for local management, in order to adopt adaptation measures to the SLR and extreme wave events induced by the global climate change.