Through time, the large ceremonial centers of the Peruvian pre-Hispanic coast have played an important role as Pachacamac, renowned for its famous oracle, which was an important site for cult and pilgrimage, where the use of water entered largely into ritual functions during Inca age and before. The sanctuary's landscape included sea, valley and lomas (ecosystem of grassy, seasonal knolls), and a complex and elaborate system of springs and canals which seem to use both the natural water table and the waters of the nearby Lurin river. In this sacred landscape there are over fifty buildings associated to springs and canals, built during a long occupation spanning over a 1000 years. This entire system must have been connected to Urpiwachaq lagoon, located to the northeast and only a few kilometers away from the sea. The origins of the lagoon and its relationship with the archaeological site evoke creation myths for the waters and marine species of the central coast. In this paper we discussed the results obtained from the geophysical investigations performed to define the water management system in the sanctuary and their connection with the lagoon. In particular, geo-electric, geomagnetic and ground penetrating radar prospections were carried out in the monumental area to determine the trajectory of the waters that drained into the lagoon from a series of ponds and canals. The interdisciplinary work in both the lagoon and monumental area provided a valuable source of information useful to better understand the history and function of the Pachacamac sanctuary in prehispanic times.