Andean societies have undergone abrupt climate changes that have affected their water resources and habitable or cultivable land. This is the case for Lake Titicaca, which has experienced fluctuations up to 20 metres during the last three millennia. Although paleoenvironmental reconstructions have provided valuable data on these lake level variations, their resolution is often not sufficient to assess their impact at the human time scale of land-use patterns. In this study, we provide a description of recent methodological developments in underwater archaeology that allows great advances in such reconstruction. Our results highlight that the level of the lake rose globally with multiple events of transgression and regression over the last two millennia. We also show that certain abrupt lake variation coincide with major transformations of the societies such as the emergence of the Tiwanaku state in the 6(th) century during a major transgression.