A three-dimensional, transient numerical model of groundwater and surface-water flow was constructed for Chamokane Creek basin to better understand the groundwater-flow system and its relation to surface-water resources. The model described in this report can be used as a tool by water-management agencies and other stakeholders to quantitatively evaluate the effects of potential increases in groundwater pumping on groundwater and surface-water resources in the basin. The Chamokane Creek model was constructed using the U.S. Geological Survey (USGS) integrated model, GSFLOW. GSFLOW was developed to simulate coupled groundwater and surface-water resources. The model uses 1,000-foot grid cells that subdivide the model domain by 102 rows and 106 columns. Six hydrogeologic units in the model are represented using eight model layers. Daily precipitation and temperature were spatially distributed and subsequent groundwater recharge was computed within GSFLOW. Streamflows in Chamokane Creek and its major tributaries are simulated in the model by routing streamflow within a stream network that is coupled to the groundwater-flow system. Groundwater pumpage and surface-water diversions and returns specified in the model were derived from monthly and annual pumpage values previously estimated from another component of this study and new data reported by study partners. The model simulation period is water years 1980-2010 (October 1, 1979, to September 30, 2010), but the model was calibrated to the transient conditions for water years 1999-2010 (October 1, 1998, to September 30, 2010). Calibration was completed by using traditional trial-and-error methods and automated parameter-estimation techniques. The model adequately reproduces the measured time-series groundwater levels and daily streamflows. At well observation points, the mean difference between simulated and measured hydraulic heads is 7 feet with a root-mean-square error divided by the total difference in water levels of 4.7 percent. Simulated streamflow was compared to measured streamflow at the USGS streamflow-gaging station-Chamokane Creek below Falls, near Long Lake (12433200). Annual differences between measured and simulated streamflow for the site ranged from -63 to 22 percent. Calibrated model output includes a 31-year estimate of monthly water budget components for the hydrologic system. Five model applications (scenarios) were completed to obtain a better understanding of the relation between groundwater pumping and surface-water resources. The calibrated transient model was used to evaluate: (1) the connection between the upper- and middle-basin groundwater systems, (2) the effect of surface-water and groundwater uses in the middle basin, (3) the cumulative impacts of claims registry use and permit-exempt wells on Chamokane Creek streamflow, (4) the frequency of regulation due to impacted streamflow, and (5) the levels of domestic and stockwater use that can be regulated. The simulation results indicated that streamflow is affected by existing groundwater pumping in the upper and middle basins. Simulated water-management scenarios show streamflow increased relative to historical conditions as groundwater and surface-water withdrawals decreased.