In coastal areas of the globe, open shell matrix sites are commonly used to establish regional chronologies of human occupation and identify patterns of cultural change, particularly for the Holocene, post-sea-level stabilisation period. Despite this, many basic sedimentary analyses that are routinely applied to rockshelter deposits (e.g. geophysical characterisation, particle size etc) are rarely applied to these sites. Magnetic susceptibility, occasionally used in rockshelters, has never been used to investigate shell matrix sites in Australia, despite several international studies identifying its efficacy for other types of open sites. This paper reports a pilot project applying a range of conventional sedimentary and archaeological analyses, as well as magnetic susceptibility at three anthropogenic shell mounds on Mornington Island, Gulf of Carpentaria, Australia. Results are compared to, firstly, assess site integrity and, secondly, to ascertain whether magnetic signatures are related to cultural or natural site formation processes. The results establish that the mounds were repeatedly visited, despite the archaeological evidence, including radiocarbon ages, suggesting effectively ‘instantaneous’ deposition. This has important implications for studies of other shell mounds where the limitations of radiocarbon dating precision may also mask multiple deposition events.