Abstract. Sea level oscillation during the Quaternary played a major role in the geomorphology and vegetation dynamics of coastal areas in southern Brazil, encompassing ecosystems that often have a unique biodiversity. Understanding the natural evolution of these areas is essential for decision-making of land use regulations towards sustainable development as well as to preserve the uniqueness of the coastal ecosystems. The southern Brazil coastal plain is formed by marine, transitional and continental Quaternary deposits controlled by relative past variations of the sea level. These variations shaped the coastal landscape and influenced the development of different Atlantic Rainforest formations, such as mangroves and restingas. In particular, the restinga formation corresponds to a specific ecosystem that covers sandy soils of marine and fluvial-marine origin formed during the Quaternary on the Brazilian coastal plain. In this contribution, we present high-resolution palynological and stable isotope data from a Holocene core retrieved from the coastal plain of the Santa Catarina Island (southern Brazil). We were able to identify four different environmental zones in the last 6500 yr BP. The first zone (6500–2820 cal yr BP) is characterized by a lagoon with large marine water influence. Notably, the observed dinoflagellate cyst association suggests that marine waters entering the region had its origin in the relatively warm saline Brazil Current waters. During the second zone (2820–1480 cal yr BP), marine water contribution to the lagoon decreased until it became disconnected with the sea. The third zone (1480–520 cal yr BP) was marked by the decrease of the water level until it dried out and led to the colonization of herbaceous vegetation over the palaeo-lagoon. The last zone (520 cal yr BP–recent) is characterized by the consolidation of the coastal plain Atlantic Rainforest (restinga vegetation). Our results form an example of the strong sensitivity of southern Brazilian ecosystem change caused by relative sea level variations. As such, it might contribute to the debate about potential effects of current climate change induced by global sea level variations.