Little is known about cultural change on the inlets of the northern subcoastal plains of the Alligator Rivers region during the transition period between sea-level highstand c.8,000 BP and the establishment of freshwater wetlands (c.2,000 BP to present). The research presented here begins to fill this gap by illustrating differences in Indigenous land-use at two sites only a few kilometres apart and both dating to c.1,000 years ago. Located on the lower reaches of the South Alligator River within what is now Kakadu National Park, the earth mound Myaranji 1 and the shell midden Djindibi 1 provide a snapshot of settlement and subsistence strategies practiced on the floodplains in the late Holocene. This paper presents the analyses of the cultural materials recovered from these two open sites, including those of invertebrate and vertebrate faunal remains, shell and stone artefacts, and pigment on artefacts. Interpretation of the data suggests that occupation was relatively short-lived. Differential representation of food resources indicates that each site was occupied in different seasons. Both local manufacture and regional connectivity are suggested by ochre use and stone artefact working. Evidence from other regional sites implies a subsequent focus for settlement to the south and east.