Malarrak 1 is currently the northernmost excavated rockshelter on the Australian mainland, located in the Wellington Range in north western Arnhem Land. The site contains a rich late Holocene deposit, with extensive contact rock art, stone artefacts, shell, bone, contact materials, ancestral human remains, and other cultural material. Excavation of the Malarrak 1 rockshelter and analysis of its sediments revealed many impacts on site formation processes within the deposit. We attribute the disturbance to possible erosion or sediment deposition during periods of intense rainfall and also to the construction of timber structures within the site. This is supported by modern and historical observations and is the focus of this paper. The extent of the disturbance to Malarrak 1 provides a cautionary tale for other excavations in the region that may be affected by similar Indigenous site occupation, as these anthropogenic activities enhance the risk of further impacts arising from biological and geomorphological processes that can impinge on the stratigraphic integrity of the cultural deposits.