The Incas built the water supply channel at a relatively steady level, depending on gravity flow to take the water from the spring to the city center. They used stone blocks to build a channel that ranged from 10 to 16 centimeters deep and 10 to 12 centimeters wide at the bottom. Wright's team concluded that the channel's nominal design capacity was about 300 liters per minute- more than twice the typical yield of 25 to 150 liters per minute of the primary and secondary springs.

The channel descends the mountain slope, enters the city walls, goes through the agricultural sector, then crosses an inner wall and enters the urban sector, where it feeds a series of 16 fountains known as the "Escalera de las Fuentes" (stairway of the fountains). The fountains are publicly accessible and partially enclosed by walls about 1.2 meters high, except for the lowest, which is a private fountain for the "Templo del Cóndor" (Condor's Temple), having higher walls. At the head of each fountain, a cut stone conduit channels the water to a rectangular spout, which was so shaped to create a water jet suitable for filling an aryballo, a typical Inca clay water jug used by the Incas for water collection and transportation. The water is collected in a stone basin carved into the rock of the mountain. Then, it enters a round drain that delivers it to the access channel for the next fountain.

Wright and his team studied the fountains extensively, conducting hydraulic flow tests and measuring the channels and outlets. They concluded that the Incas designed the fountains to operate optimally with a flow of about 25 liters per minute, but the fountains could operate with such low flows as 10 liters per minute and could handle a maximum flow of 100 liters per minute. The team found water control points at two spots along the channel, where excess water would have spilled over onto the agricultural terraces or into Machu Picchu's main drain before reaching the fountains.

Wright's study of Machu Picchu's hydrology and hydraulic engineering led him to conclude that the Incas understood the importance of having drinking water. The surface drainage system generally drove the agricultural and urban storm water runoff away from the water supply canal. Wright also noted that the Inca apparently did not use the fountains for bathing. The emperor, for example, had a bathing room with a separate drain. Therefore, water used for bathing did not re-enter the water supply.

In 1998, Wright's team discovered another, previously unknown series of fountains on the eastern side of the ridge, downhill from Machu Picchu. These fountains received their water not from the channel but from intercepted groundwater drainage. While elaborate spring works were not necessary here, Wright says, "the Inca would have had to identify the groundwater flow locations during dry-weather and concentrate this flow for use in the fountains."
Adjacent to some of the fountains, an important trail, also discovered by Wright's team, connected Machu Picchu to the Urubamba River, in the valley, at the height of the dense forest. The team restored the water flow to this second series of fountains probably for the first time in 450 years.

How successful were the Incas in planning their water supply? Observers have suggested different theories to explain why the Incas abandoned Machu Picchu. Some suggested that a water shortage forced the Incas to leave. Wright says his research rejects that theory.

A hydrological analysis showed that the yield of the primary spring was related to the amount of rainfall. To determine rainfall levels during the time the Incas occupied Machu Picchu (from 1450 to about 1540), Wright analyzed ice core data coming from a glacier found 250 km to the southeast. The analysis suggested that Machu Picchu annually received nearly 2,000 centimeters of rainfall, and that in the final decade of occupancy rainfall actually increased.

Wright determined that a 10 liters per minute flow for the fountains during the dry months would have been enough to meet the needs of the population, which may have varied from 300 to a maximum of 1,000 people when the emperor was in residence. In a dry year's winter, Wright says, the Incas may have experienced a temporary water shortage. But his discovery of the trail that leads to the Urubamba River seemed to confirm that the Incas in this case would have used the river as a secondary water source. Consequently, Wright concluded that a water shortage was not the explanation for Machu Picchu's abandonment.