Water management substantially alters natural regimes of streamflow through modifying retention time and water exchanges among different components of the terrestrial water cycle. Accurate simulation of water cycling in intensively managed watersheds, such as the Yakima River Basin (YRB) in the Pacific Northwest of the U.S., faces challenges in reliably characterizing influences of management practices (e.g., reservoir operation and cropland irrigation) on the watershed hydrology. Using the Soil and Water Assessment Tool (SWAT) model, we evaluated streamflow simulations in the YRB based on different reservoir operation and irrigation schemes. Simulated streamflow with the reservoir operation scheme optimized by the RiverWare model better reproduced measured streamflow than the simulation using default SWAT reservoir operation scheme. Scenarios with irrigation practices demonstrated higher water losses through evapotranspiration (ET), and matched benchmark data better than the scenario that only considered reservoir operations. Results of this study highlight the importance of reliably representing reservoir operations and irrigation management for credible modeling of watershed hydrology. Both SWAT and RiverWare are community-based and have been widely tested and applied for reservoir operations and agricultural watershed modeling in regions across the globe. As such, the methods and findings presented here hold the promise to apply to other intensively managed watersheds to enhance water resources assessment.