The diverse Holocene morphological features along the south coast of the state of Santa Catarina include lagoons and residual lakes, a barrier, a delta (constructed by the Tubarão River), and pre-existing incised valleys that have flooded and filled. This scenario contains the sedimentary record of the transition from a bay to a lagoon system, which occurred during the rise and subsequent semi-stabilisation of the relative sea-level during the Holocene. The geomorphological evolution of this area was investigated using a combination of morphology, stratigraphic analysis of rotary push cores, vibracores and trenches with radiocarbon dating, taxonomic determination and taphonomic characterisation of Holocene fossil molluscs. Palaeogeographic maps were constructed to illustrate how the bay evolved over the last 8000years. The relative sea-level rise and local sedimentary processes were the prime forcing factors determining the depositional history and palaeogeographic changes. The Holocene sedimentary succession began between 8000 and 5700cal BP with the deposits of transgressive sandsheets. These deposits correspond to the initial marine flooding surface that was formed while the relative sea-level rose at a higher rate than the input of sediments, prior to the formation of the coastal barrier. The change from a bay to a lagoon system occurred around 5700 and 2500cal BP during the mid-Holocene highstand with the formation of the barrier and with the achievement of a balance between sea-level rise and sedimentary supply. Until 2500cal BP, the presence of this barrier, the following gentle decline in sea level and the initial emergence of back-barrier features restricted the hydro-dynamic circulation inside the bay and favoured an increase in the Tubarão River delta progradation rate. The final stage, during the last 2500years, was marked by the increasing back-barrier width, with the establishment of salt marshes, the arrival of the delta in the back-barrier, and the advance of aeolian dunes along the outer lagoon margins. This study shed light on the mechanisms of coastal bay evolution in a setting existed prior to the beginning of barrier–lagoon sedimentation.