Elongate, rock-framed Santa Catarina Island partly encloses a low-energy marine embayment that communicates with the ocean via narrow, rock-bounded inlets with ebb and flood-tide deltas. The bay shoreline consists of low-energy sandy beaches, strandplains, mangroves and bayhead deltas while the exposed Atlantic shoreline comprises a series of headland-embayment littoral cells in a linked, north-directed longshore drift system. New and previously published seismic stratigraphic investigations enable assessment of the palaeogeographic/geomorphic evolution of the area since the early Holocene. At a sea level of ca. −50 m a sandy mainland-attached shoreline complex (dune and beach) developed on a coastal plain setting some 6–7 km offshore of the present shoreline. North of the island, a barrier island and tombolo were formed in a coastal re-entrant adjacent to the northern entrance to Florianopolis Bay. The open coast beach/dune system was overstepped by rapid sea-level rise during MWP-1B whereas the barrier island and tombolo continued to accrete until MWP-1C when they too were overstepped. The back-island embayment contains up to 40 m of sediment overlying an irregular bedrock surface. It was initially flooded during MWP-1C and the early muddy sedimentation suggests a distal, sheltered marine embayment. The subsequent development of many large bioherms on bedrock and mud suggests a change to more fully marine conditions as sea-level continued to rise. In the North Bay, these were subsequently enveloped by tidal dunes migrating north from the mid-bay. The vertical stacking of 3-D and 2-D sandy bedforms suggests that a tidal strait had developed with strong tidal currents radiating from a constriction in the vicinity of modern Florianopolis City. The strong tidal currents may be linked to the Holocene sea-level high that is well documented for this region. A fall in sea level from this highstand, coupled with accumulation of tidal strait sediments, reduced the tidal prism and strength of tidal currents in the bay. At the same time, regressive beachridge plains developed in open coast and bay environments. This coincided with development of the contemporary tidal inlet complexes at the north and south outlets of the bay. As a consequence, the upper surface of the tidal strait sand deposits experienced tidal ravinement and the bay switched to a sheltered back-barrier environment dominated by deposition of mud and silt which blanket the contemporary bay floor. The tidal inlets sequestered sand from the littoral drift system in ebb and flood-tide deltas, which created breaks in the longshore drift system, causing littoral sediment to accumulate at the north of the island in a series of spits, and promoting strandplain development south of the island.