The Walla Walla basin lies in an arid region of Eastern Washington and Oregon. A large portion of the area is devoted to agricultural production, relying on irrigation water diverted from the Walla Walla River and underlying aquifers occurring within Quaternary and Mio-pliocene era gravel deposits, as well as a supplemental source from the Columbia River Basalt formation. Heavy water demand over summer months has resulted in a fully allocated surface water supply and significant drawdown in groundwater levels. The Walla Walla River also hosts two salmonid species listed as threatened under the endangered species act and entitled to federal protection. Specific questions have emerged regarding regional water supply as stakeholders work towards management strategies that meet water user demands, well also addressing concerns such as groundwater depletion and fish habitat. Currently, there are proposals aimed at increasing water use efficiency such as the lining of permeable canal beds and the expansion of a shallow aquifer recharge program. Effective implementation of such strategies, in part, relies on understanding the interactions between surface water and groundwater within this region. This project used the distributed hydrologic model, Integrated Water Flow Model (IWFM), for simulating surface and subsurface flows over a portion of the Walla Walla River basin spanning from Milton Freewater, Oregon to west of Touchet, Washington. This application of IWFM uses a grid with an average spacing of 100 x 100 meters over the 230 square kilometer model area. The model was developed and calibrated using data from 2007 through 2009, with 2010 data to be used as a data set for validation. Data collection has been a collaborative effort between a research team from Oregon State University and the Walla Walla Basin Watershed Council (WWBWC). This thesis provides explanation and documentation of model development. This includes details of data collection and processing for groundwater and surface water conditions, estimation of initial and boundary conditions, parameter calibration, model validation, and error analysis. Data sources include federal and state agencies, a gauge network managed by the WWBWC, and geologic research primarily performed by Kevin Lindsey of GSI Water Solutions with support of the WWBWC. Parameters have been independently determined from field measurements whenever possible. Otherwise they were estimated using established methods of hydrologic analysis, values drawn from previous regional studies, or the process of model calibration. Outputs include detailed hydrological budgets and hydrographs for groundwater and surface water gauges. The calibrated model has an overall correlation coefficient of 0.59 for groundwater and 0.63 for surface water. The standard deviation for groundwater is 3.2 meters at 62 well locations and surface water has a mean relative error of 22.3 percent at 34 gauges. This model intended as a tool for formulating water budgets for the basin under present conditions and making predictions of systemic responses to hypothetical water management scenarios. Scenarios of increased inputs into the Locher Road aquifer recharge site and conversion of irrigation district canals into pipelines are presented. / Graduation date: 2012