The prehispanic site of Tiwanaku, located in northeastern Bolivia, was the focus of many studies during the past few decades. However, much of the site remains unexplored, leaving many questions unanswered about the location of dense archaeological deposits, the nature of urban organization, and water management strategies—specifically those located in the eastern sector of the Akapana Pyramid. Orthophoto mosaics and Digital Elevation Models derived from drone imagery helped identify archaeological features and anthropogenic mounds. New magnetic survey produced with a cesium gradiometer was merged with previous surveys (fluxgate and cesium gradiometer). The integration of maps and plans from six areas of a previous archaeological investigation within a common Geographical Information System helped relate geophysical anomalies to archaeological features. Our results demonstrate a high level of urban organization associating monumental buildings to open ritual spaces and to densely populated areas during Tiwanaku IV (500–800 CE) and V (800–1100 CE). The complexity of the urban organization is also demonstrated by landscape modifications such as a complex water management system and at least three terraces that augmented the monumentality of the Akapana Pyramid This interdisciplinary approach, innovative in Bolivia, provides new insight into one of the most significant archaeological sites in the Andes.