A numerical flow model (MODFLOW) of the groundwater flow system in the primary aquifers in northern Arizona was developed to simulate interactions between the aquifers, perennial streams, and springs for predevelopment and transient conditions during 1910 through 2005. Simulated aquifers include the Redwall-Muav, Coconino, and basin-fill aquifers. Perennial stream reaches and springs that derive base flow from the aquifers were simulated, including the Colorado River, Little Colorado River, Salt River, Verde River, and perennial reaches of tributary streams. Simulated major springs include Blue Spring, Del Rio Springs, Havasu Springs, Verde River headwater springs, several springs that discharge adjacent to major Verde River tributaries, and many springs that discharge to the Colorado River. Estimates of aquifer hydraulic properties and groundwater budgets were developed from published reports and groundwater-flow models. Spatial extents of aquifers and confining units were developed from geologic data, geophysical models, a groundwater-flow model for the Prescott Active Management Area, drill logs, geologic logs, and geophysical logs. Spatial and temporal distributions of natural recharge were developed by using a water-balance model that estimates recharge from direct infiltration. Additional natural recharge from ephemeral channel infiltration was simulated in alluvial basins. Recharge at wastewater treatment facilities and incidental recharge at agricultural fields and golf courses were also simulated. Estimates of predevelopment rates of groundwater discharge to streams, springs, and evapotranspiration by phreatophytes were derived from previous reports and on the basis of streamflow records at gages. Annual estimates of groundwater withdrawals for agriculture, municipal, industrial, and domestic uses were developed from several sources, including reported withdrawals for nonexempt wells, estimated crop requirements for agricultural wells, and estimated per capita water use for exempt wells. Accuracy of the simulated groundwater-flow system was evaluated by using observational control from water levels in wells, estimates of base flow from streamflow records, and estimates of spring discharge. Major results from the simulations include the importance of variations in recharge rates throughout the study area and recharge along ephemeral and losing stream reaches in alluvial basins. Insights about the groundwater-flow systems in individual basins include the hydrologic influence of geologic structures in some areas and that stream-aquifer interactions along the lower part of the Little Colorado River are an effective control on water level distributions throughout the Little Colorado River Plateau basin. Better information on several aspects of the groundwater flow system are needed to reduce uncertainty of the simulated system. Many areas lack documentation of the response of the groundwater system to changes in withdrawals and recharge. Data needed to define groundwater flow between vertically adjacent water-bearing units is lacking in many areas. Distributions of recharge along losing stream reaches are poorly defined. Extents of aquifers and alluvial lithologies are poorly defined in parts of the Big Chino and Verde Valley sub-basins. Aquifer storage properties are poorly defined throughout most of the study area. Little data exist to define the hydrologic importance of geologic structures such as faults and fractures. Discharge of regional groundwater flow to the Verde River is difficult to identify in the Verde Valley sub-basin because of unknown contributions from deep percolation of excess surface water irrigation.