Geographical Information Systems (GIS) provide an essential element in modern paleoanthropological inquiry through their ability to integrate a diverse range of data within a multidimensional spatial framework which can be used for data storage, analysis and modeling. One of the challenges of creating such a framework is the integration of legacy and new data (collected with digital technologies) at large sites with a long history of research. The Sterkfontein Caves, located in the Cradle of Humankind, is the richest Australopithecus-bearing locality in the world and has been the focus of intense palaeoanthropological research for the past 80 years. A diverse range of spatial data has been collected over this history and future integrative research necessitates the development of a unified, cohesive 3D GIS framework. In this paper we describe three phases of work undertaken to implement such a framework and discuss the next steps in its development and utilization for spatial analyses.