Late Holocene patterns of change in occupation and use of islands along the eastern coast of Queensland have long been debated in terms of various drivers, though much of this discussion relates to regions south of Cairns, with comparatively little study of the far northern Great Barrier Reef islands. The numerous middens, stone arrangements and art sites on Lizard Island suggest long-term use by Indigenous people, but recent discoveries of pottery give tantalising glimpses of a prehistoric past that may have included a prehistoric economy involving pottery. Here we review previous archaeological surveys and studies on Lizard Island and report on new archaeological and palaeoenvironmental studies from the Site 17 midden at Freshwater Beach, with an oldest date of 3815–3571 cal BP. We identify two major changes in the archaeological and palaeoenvironmental records, one associated with more recent European influences and the other at c.2000 cal BP. Pottery from the intertidal zone is as yet undated. When dates become available the relationship between the Site 17 results reported here and the use of pottery on the island may be clarified.