The Shark Bay environment has been shaped by Quaternary geologic events. The geomorphology of the embayment reflects the geometry and lithology of underlying rock units. The western and central parts of the region are underlain by dune rocks of Pleistocene age, and the numerous inlets and gulfs in the area are interdune depressions which were flooded by postglacial transgression. The eastern shore of the embayment is an alluvial coastal plain in the north and a terrain of flat-lying Cretaceous limestone and dolomite in the south.

There were two phases of dune building in the early Pleistocene. The sediments of the Peron Sandstone were deposited during the first of these phases. This formation is present in the central area and is composed of red quartz sandstone. The second dune phase completed the basic architecture of the embayment. Large ridges of calcareous eolianite are present along the western perimeter. The eolianite units are grouped in one formation, the Tamala Eolianite.

The ancestral dune landscape was flooded by the sea in three separate marine transgressions during the later part of the Quaternary. The transgressions, in order of decreasing age, are the Dampier marine phase, the Bibra marine phase, and the Holocene-Recent marine phase. The Dampier and Bibra transgressions occurred during the Pleistocene; they are represented by sequences of marine carbonate strata which crop out around the margins of the embayment and also lie beneath postglacial sediments in offshore areas. The outcropping Pleistocene rocks are intertidal and shallow subtidal facies whose distribution virtually defines the paleogeography of the embayment. The embayment during both the Dampier and Bibra phases was essentially similar to the present embayment. The transgressive depo its are separated by erosional unconformities marked by weathering phenomena, including the development of soils and calcrete.

The environments associated with the Pleistocene transgressive phases were similar to the present environments of Shark Bay, and there is a general similarity of sediments and fossil assemblages between Recent and Pleistocene layers. Because the shorelines of Pleistocene phases were roughly coincident with the present datum, similar lithologies and fossil assemblages are repeated in stratigraphic sections.