•Multidisciplinary approach cross-combined to previous geomorphological maps.•Watercourse are associated to pre-Columbian agricultural structures.•Regressive pattern of the Titicaca Lake coastline since mid-20th century.•Major alluvial evolution since mid-20th century.•First synthetized geomorphological and geoarchaeological map of the watershed. The Altiplano and more specifically the Titicaca circum-lake sector have recorded several major landscape transformations. In particular, changes in the lake water level lead to a significant vulnerability and contributed to the development of flexible and diverse agropastoral activities of the pre-Columbian and current populations to climate change. The Tiwanaku River, particularly because of the presence of the pre-Columbian Tiwanaku site, has been the subject of several research studies aimed at characterizing the environment of the archaeological site. Here we propose a new synthesis of the geomorphology of the Tiwanaku River watershed based on an interdisciplinary approach (Historical geography and remote sensing, cross combined with field survey). Our results show that the general organization of the drainage system is influenced by lake level and climatic changes. However several watercourses of the Tiwanaku River might be related to pre-Columbian agricultural or proto-urban structures. Our work allowed to estimate the regressive pattern of the coastline of Lake Titicaca and to identify major changes of the terminal and medium watercourse of the Tiwanaku River over the last 70 years.