Machupicchu, the Inca city, is located in the Eastern Cordillera of southern Peru, at 2,450 meters above sea level, and 500 m above the Urubamba River, which cuts through the Cordillera and originates a canyon with tropical mountain climate. The local substrate consists of granite outcrops and large irregularly-piled granite boulders -granitic chaos - over which the Inca city of Machupicchu was built. The Plio-Quaternary geological evolution shows a very fast exhumation of the Cordillera which determined the geodynamic phenomena, the same that originated the current geomorphology and now affect the Inca city. During Inca occupation, the drainage system of terraces and thatched-roof buildings allowed an efficient evacuation of the abundant rainfall water. However, this is no longer the case: buildings have no roof and most of the terrace drainages are not functional, leading to strong infiltration, surface erosion, suffusion, subsidence, rock falls and shallow landslides. Detailed geological surveys and site-specific studies in several areas of the city allow suggesting recommendations for an adequate evacuation of rain water with drainages and impermeable surfaces to avoid infiltration and surface erosion.