This paper provides a paleoenvironmental reconstruction of a Late Quaternary lagoon system in the Jaguaruna region of Santa Catarina state, southern Brazil. Integrated results of bulk sedimentary organic matter characterization (δ13C, δ15N and C/N), microfossil (pollen and diatom) and grain-size analysis from three shallow cores (∼2.5 m depth) allowed us to propose an evolving paleogeographic scenario in this coastal region for the last ca. 5500 cal a BP. The lagoonal system in this area was more extensive during the mid-Holocene than today, with a gradual and continuous lagoon–sea disconnection until the present. We add to the debate regarding relative sea-level (RSL) variations for the Brazilian coast during the Holocene and discuss the importance of sedimentary dynamics for interpreting changes in coastal ecosystems. The multi-proxy analysis suggests that changes in coastal ecosystems could be directly related to local sedimentary processes, which are not necessarily linked to RSL fluctuations and/or to climatic variations. Copyright © 2011 John Wiley & Sons, Ltd.