Evidence from Liang Bua, a limestone cave on the island of Flores in East Indonesia, provides a unique opportunity to explore the long term relationship between hominins and their environment. Occupation deposits at the site span ∼95 ka and contain abundant stone artefacts, well preserved faunal remains and evidence for an endemic species of hominin: Homo floresiensis. Work at the site included detailed geomorphological and environmental analysis, which has enabled comparisons to be drawn between changes in the occupational intensity in the cave, using stone tool and faunal counts, and changes in the environmental conditions, using the characteristics of the sedimentary layers in the cave and speleothem records. These comparisons demonstrate that H. floresiensis endured rapidly fluctuating environmental conditions over the last ∼100 ka, which influenced the geomorphological processes in the cave and their occupational conditions. The intensity of occupation in the cave changed significantly between 95 and 17 ka, with peaks in occupation occurring at 100-95, 74-61 and 18-17 ka. These correlate with episodes of channel formation and erosion in the cave, which in turn correspond with high rainfall, thick soils and high bio-productivity outside. In contrast, periods of low occupational intensity correlate with reduced channel activity and pooling associated with drier periods from 94 to 75 and 36 to 19 ka. This apparent link between intensity of hominin use of the cave and the general conditions outside relates to the expansion and contraction of the rainforest and the ability of H. floresiensis to adapt to habitat changes. This interpretation implies that these diminutive hominins were able to survive abrupt and prolonged environmental changes by changing their favoured occupation sites. These data provide the basis for a model of human-environment interactions on the island of Flores. With the addition of extra data from other sites on Flores, this model will provide a greater understanding of H. floresiensis as a unique human species.