Seventeen vibrocores from the inner part of Joseph Bonaparte Gulf off northwestern Australia penetrate a range of marine and marginal-marine sediments deposited in the post-glacial transgression and highstand. Ranging from gravelly sand to fine silt, these sediments contain a diverse fossil blota dominated by molluscs and bryozoans, but also including ostracods and foraminifers. Minor components include solitary corals, echinoids, soft coral and sponge spicules, wood debris and bone fragments. The blota can be divided into five major marine or marginal-marine environments (intertidal, lagoonal, estuarine, strandline and shelf) and one terrestrial (riverine) environment. The intertidal environment contains four sub-assemblages (mangroves, salt marsh, mud flat and sand flat) and the shelf environment six sub-assemblages (hard substrate inner shelf, sandy substrate inner shelf, muddy substrate inner shelf, epiphytic, inshore and oceanic). The most useful organisms for palaeo-environmental reconstruction are bryozoans for differentiating various shallow-marine substrates, and foraminifers and ostracods for defining water depths, euryhaline, freshwater and oceanic influences. Palynomorphs were the only microfossils capable of providing control on terrestrial environments. The scarcity of marine plankton and the dominance of terrestrial palynomorphs in these marine sediments provides a salutary warning of the dangers of relying on plant microfossils alone when no independent environmental data are available to test the interpretation. The mollusc and bryozoan blota in the inner part of Joseph Bonaparte Gulf superficially resembles the bryomol assemblage of cool-water shelves. This biotic assemblage is the result of turbidity rather than water temperature. The turbidity suppresses the photosynthetic, zooxanthellate and hermatypic organisms allowing molluscs, bryozoans and other apparently cool-water biotic elements to dominate.