Archaeological evidence suggests that humans have lived in the Verde Valley for at least 10,000 years. The earliest signs of permanent settlement in the area appear quite a bit later, however, around 600 CE.
The ruins of several prehistoric dwellings are scattered in and around the rim of the Well. Their erstwhile inhabitants belonged to several indigenous American cultures that are believed to have occupied the Verde Valley between 700 and 1425 CE, the foremost of which being a cultural group archaeologists have termed the Southern Sinagua.The earliest of the ruins located on the property (with the exception of the irrigation canal), a "pithouse" in the traditional Hohokam style, dates to about 1050 CE. More than 50 countable "rooms" are found inside the park boundaries; it is likely that some were used for purposes other than living space, including food storage and religious ceremonies.
The Sinagua people, and possibly earlier cultures, intensively farmed the land surrounding the Well using its constant outflow as a reliable source of irrigation. Beginning about 700 CE, the Well's natural drainage into the immediately adjacent Wet Beaver Creek was diverted into a man-made canal running parallel to the creek, segments of which still conduct the outflow today. The prehistoric canal, estimated at nearly seven miles in length, likely drained into a network of smaller lateral canals downstream, supplying perhaps as much as 60 acres of farmland with water. The route of the modern canal is partly original, especially close to the outlet, but large portions have been re-routed over time as irrigation needs have changed. Much of the abandoned original route is still visible within the park, however, as the warm water emerging from the Well contains a high concentration of lime, which over many centuries was deposited along the canal walls as the water cooled downstream; the accumulated lime has since hardened into a cement-like coating.