Most of the water in the aquifer is derived from the downward migration of water from the overlying Coconino aquifer. Shale units within the limestone aquifer impede the downward migration of water while solution cavities and fracture zones provide avenues for lateral movement. A large part of the groundwater moves northward and is discharged from springs along the Little Colorado and Colorado Rivers and Havasu Creek. The location of the groundwater divide in the southern part of the basin is unknown. Groundwater development in the basin is small and limited by the great depth to water and by the low yield to wells.
Yields are highly dependent upon fractures, faults, and solution channels.
The Moenkopi and Chinle Formations, volcanic rocks, and sedimentary deposits which overlie the Coconino and limestone aquifers, provide locally important sources of water for domestic and livestock purposes but do not contain water over large areas. For example, Fort Valley, near Flagstaff, is in a small volcanic basin where the regional aquifer in the Redwall Limestone is at a depth of about 2,000 feet below land surface. The perched groundwater in the shallow sediments and lava flows are rather unstable during low precipitation periods. Similarly, groundwater in the lava flows near Williams is also drought sensitive and cannot provide a dependable supply for larger developments.