Open-air surface accumulations and scatters of material cultural remains often are perceived as less-reliable archaeological archives, where it is difficult to distinguish anthropogenic versus geogenic formation processes or to assess their specific effects on the integrity of archaeological records. Here we analyze the depositional histories of three Middle Paleolithic open-air sites in the Negev desert of Israel, combining archaeological and geomorphological methods to create a conceptual model of multi-scale effects on the archaeological remains. Relying on the long research history in archaeology and geomorphology in the Negev, we show that integration of archaeological and geomorphological methodologies provides nuanced insights to our understanding of the archaeological record. The links established between regional and local geomorphic processes and lithic taphonomy by applying such a multi-scale analysis further allow back-tracking environmental processes from flint taphonomic attributes. Placing each site within the range of regional and local processes of exposure and burial by using informed and critically evaluated data helps to create a robust regional archaeological data base. We suggest that our approach is useful in other arid zone contexts and may have implications for understanding Pleistocene population movements across such regions.