Aboriginal peoples have managed Australian landscapes for millennia; however, deep-time paleoecological evidence of the nature of landscape modification remains rare. The Fleurieu Group of islands in Bass Strait was one of the areas actively used by Aboriginal people in lutruwita (Tasmania), until forced dispossession of their lands due to European colonization occurred over 230 years ago, with subsequent land use including leaseholder pastoralism and nature conservation. There are emerging opportunities for greater input from Aboriginal people into land management of the islands now and into the future. This investigation of the long-term human–island ecosystem interactions in the area is aimed at providing a greater understanding of the impact of land-use changes on biodiversity and ecosystem change through time. Holocene multi-proxy paleoecological records from the islands show periods of low to high intensity land use, with the highest intensity periods occurring around 8500–6500 BP and the last 2000 years. Aboriginal land use in the past ∼2000 BP promoted a complex mosaic biodiverse landscape and provides a baseline for current and future land management on the islands and elsewhere in Tasmania.