Cape York Peninsula in the far north east of Australia is the closest mainland point to Papua New Guinea and could well prove to be the site of initial colonisation of the continent >60,000 years ago. This tropical landscape of endemic flora and fauna has been isolated from Australia’s urban and industrial activity for the past 200 years, remaining remote and to a large degree unpopulated. The lack of recent development has resulted in very few archaeological investigations in the region, leaving gaps in our understanding of Cape York prehistory. This thesis provides new narratives on prehistory in the region through bioarchaeological and biogeochemical studies of Aboriginal human remains. These investigations have been framed and directed by Indigenous communities throughout Cape York and represent a form of community bioarchaeology. Biogeochemistry has been used globally in archaeology for over 40 years, however in Australia these techniques remain underutilised. Being a destructive, complicated and expensive set of analyses, with the added complexity of piecing together a meaningful narrative from small datasets, has resulted in few Australian archaeological isotope studies. The research presented here is one of the most extensive archaeological isotope projects conducted in the region to-date. In partnership with Aboriginal communities from Cape York we examined prehistoric/historic burials and mortuary cave internments from savannah and continental island settings. Landscape strontium isotope ratio (87Sr/86Sr) baseline data were also gathered for comparison with human results to investigate mobility and community structure. This thesis is presented as five scientific studies that have been prepared as chapters in a publication format for submission to international peer reviewed journals. I have conducted the fieldwork, historical research, scientific analyses and writing of all of these documents with editing, field/technical assistance and funding attributed to my supervisory team and co-authors. Preliminary chapters detail the excavation and analyses of human remains from the Flinders Islands and Gulf Plains of Cape York, discussing them within archaeological and historical contexts. The following study measures 87Sr/86Sr in surface soils, vegetation, waterways and mammalian fauna to test the reliability of predicting human provenance in Cape York, taking geological, seasonal and weathering processes into account. Regional portions of this baseline data are then analysed in detail in two case studies comparing human tooth enamel and dentine 87Sr/86Sr, carbon (δ13C) and oxygen (δ18O) isotope signatures to interpret prehistoric and colonial period mobility and provenance. This thesis forms part of an overarching ARC project: (ARC Linkage: LP140100387) to test scientific techniques for provenancing Aboriginal ancestral remains. The studies presented here demonstrates the research value of isotope geochemistry in Australian bioarchaeology and provides a foundation for future repatriation of unprovenanced Aboriginal remains.