The northern portion of the coastal plain of the Rio Grande do Sul State (southernmost Brazil) comprises an outer sandy barrier that protects a complex lagoon system formed during the Holocene. The terraces of three different lagoons (Gentil, Malvas and Pinguela) formed along their margins record the depositional processes and the relative base level changes over the past 5000 yr. Therefore, our main objective was to characterize and quantify base level fluctuations from the study of these terraces, to correlate them to sea-level changes and to describe the depositional architecture related to the distinct sea-level stages (high-resolution sequence stratigraphy). Satellite images, topographic and GPR profiles, auger holes and radiometric dating were used. The main results indicate a close relationship between relative base level and relative sea-level changes, a stillstand period just after the last transgressive maximum (4840–4650 cal yr BP) and a subsequent overall relative sea-level fall of about 3 m. Both a normal (highstand systems tract) and a forced regression (falling-stage systems tract) controlled the geological record preserved in the terraces. The highstand (older terrace) is characterized by agradational bedding, whereas the falling stage comprises three progradational sets (terraces) bounded by erosive surfaces related to smaller-scale sea-level drops.