The Miocene Columbia River Basalt Group and younger sedimentary deposits of lacustrine, fluvial, eolian, and cataclysmic-flood origins compose the aquifer system of the Quincy Basin in eastern Washington. Irrigation return flow and canal leakage from the Columbia Basin Project have caused groundwater levels to rise substantially in some areas. Water resource managers are considering extraction of additional stored groundwater to supply increasing demand. To help address these concerns, the transient groundwater model of the Quincy Basin documented in this report was developed to quantify the changes in groundwater flow and storage. The model based on the U.S. Geological Survey modular three-dimensional finite-difference numerical code MODFLOW uses a 1-kilometer finite-difference grid and is constrained by logs from 698 wells in the study area. Five model layers represent two sedimentary hydrogeologic units and underlying basalt formations. Head-dependent flux boundaries represent the Columbia River and other streams, lakes and reservoirs, underflow to and (or) from adjacent areas, and discharge to agricultural drains and springs. Specified flux boundaries represent recharge from precipitation and anthropogenic sources, including irrigation return flow and leakage from water-distribution canals and discharge through groundwater withdrawal wells. Transient conditions were simulated from 1920 to 2013 using annual stress periods. The model was calibrated with the parameter-estimation code PEST to a total of 4,064 water levels measured in 710 wells. Increased recharge since predevelopment resulted in an 11.5 million acre-feet increase in storage in the Quincy Groundwater Management Subarea of the Quincy Basin. Four groundwater-management scenarios were formulated with input from project stakeholders and were simulated using the calibrated model to provide representative examples of how the model could be used to evaluate the effect on groundwater levels as a result of potential changes in recharge, groundwater withdrawals, or increased flow in Crab Creek. Decreased recharge and increased groundwater withdrawals both resulted in declines in groundwater levels over 2013 conditions, whereas increasing the flow in Crab Creek resulted in increased groundwater levels over 2013 conditions.