Prior to historic times the Little Colorado River was a perennial stream, though it perhaps was intermittent on a seasonal basis as its flow was absorbed in deep sand deposits in its channel. Just downstream from Wupatki, the Little Colorado has carved an impressive canyon known as the Little Colorado Gorge. This gorge has its confluence with the Grand Canyon approximately 80 km north- northwest of Wupatki. This canyon is testament to the power of the Little Colorado, which can carry heavy floodwaters. In general, the Little Colorado River has two peaks of flow, one during the late spring when snowmelt feeds the river, and the other during the late summer 'monsoon' when thunderstorms can swell it with brown, silt-laden waters. It is unclear if prehistoric residents in the vicinity of Wupatki used the river for irrigating their fields, but they probably did. No doubt it was used for drinking water also, though it probably was not a preferred source (the water contains relatively large amounts of silt and dissolved solids, including salt.)

Wupatki Pueblo lies about 10 km west of the Little Colorado floodplain along an unnamed arroyo that joins Deadman Wash. The latter stream is the major tributary to the Little Colorado on the northeast side of the San Francisco Peaks. Paradoxically, however, Deadman Wash in recent times does not often flow with water. This is due to the geology of the San Francisco Volcanic field, which consists of very porous and fractured rock formations and features an overlying mantle of highly absorbent volcanic ash and other deposits that rapidly soak up most rainfall and snow melt. (The area around the Peaks was referred to by early Spanish explorers as the "Sierra Sin Agua" ["mountains without water"] which provides the name for the archaeological culture that inhabited the region -- the Sinagua). Thus, although the San Francisco Peaks rise to an elevation of about 12,600 ft. (3,840 m) and comprise an immense stratovolcano with a large net drainage basin that often receives copious amounts of snow and rain, local drainages do not carry large volumes of surface water. Neither Deadman Wash nor any of its tributaries in the Wupatki Basin today flow except during or immediately after the most extreme precipitation events, or when an extremely heavy snowpack melts. The runoff from the northeast side of the Peaks thus virtually never flows directly to the Little Colorado River. There is some evidence that Deadman Wash might have been a more active stream in pre-modern times, but this possibility remains to be investigated.

Known sources of reliable surface water in the Wupatki Basin are confined to the Little Colorado River itself, small ephemeral catchments in stream bottoms or on bedrock surfaces, and a series of small springs near Wupatki fed by groundwater emanating from the northeast side of the Peaks. The nearest historically documented spring is Wupatki Spring, located about 200 m west of the Pueblo. This spring flowed until the early 1960s, when it dried up. It is possible that there was another spring or seep just a few meters east of the South Ruin of Wupatki Pueblo, within the small sandstone rincon east of the Pueblo. This possibility is suggested by cemented volcanic ash deposits that appear identical to deposits seen around Wupatki Spring, and what appears to be a small check dam across the stream channel just downslope from these putative spring deposits. The existence of a spring in this location at present has not been confirmed, and is merely a possibility.

One solution to the problem of obtaining drinking water was to capture it in pottery vessels or small, intentionally built wet-weather catchments. At Wupatki Pueblo, a prehistoric pottery vessel was discovered where it had been strategically placed some 800 years ago to catch water flowing over a bedrock outcrop. During an archaeological survey, a small pottery canteen was found in the Big Hawk Valley area, resting on a bedrock outcrop where it evidently had set down and forgotten some time in the A.D. 1100s. These finds give us an understanding of the specific ways in which people captured and transported water.

Throughout the greater Wupatki area, numerous small, seasonal catchments have been discovered. These catchments (or perhaps more accurately, ponds) were built in the period of prehistoric occupation by placing rocks and earthen berms across shallow wash channels. During the summer rainy season, they would have filled with runoff long enough to allow water to be scooped from them and into pottery jars for long-term storage.

Wupatki’s residents may have found additional water at Heiser Spring, 1.5 mi. (2 km) southeast of the pueblo, Peshlaki Spring, about 2 mi. (3.2 km) southeast, and Coyote Spring (outside the current Monument boundaries), about 2.5 mi. (4.1 km) south-southeast of Wupatki.