The aim of the present study consists on the establishment of any relationship or interaction between geomorphological processes and vegetation/habitat distribution in an area with strong environmental gradients: an active saline lake in NE Spain. The resulting maps of the major geoforms and CORINE habitats within the lacustrine area were overlain to determine any significant relationships, taking into account the elevation derived from Lidar data. Whereas the geoforms resulted to have a roughly concentric distribution, the habitats appeared to be spread across different areas, and flooding frequency seemed not to be a determining factor in their altitudinal distribution. The correspondence matrix for geoforms and habitats underlined the coincidence between presently active morphodynamic units, flooding/salinity, and habitats typical of saline environments. Geomorphological units associated with the presently active shoreline dynamics host the habitats more typically related to frequent flooding and high salinity levels. The delay between geomorphological dynamics and vegetation changes, together with the opportunistic character of vegetation, promote the coexistence of different geomorphological processes and a great variety of plant communities and habitats. As a major conclusion, the present study provides a method through which a standard procedure may be set up to further determine the interaction between geomorphological processes and vegetation distribution, very useful for understanding vegetation patterns and conservation biodiversity, and the planning and managing of Natura 2000 sites.