The headwaters of the Walla Walla River lie in the Blue Mountains of northeastern Oregon. The river originates as the North and South Forks of the Walla Walla River. The surrounding forested land holds a network of hiking and mountain-biking trails. The confluence of the North and South Forks lies east of Milton–Freewater, Oregon. The river flows eastward to reach Milton–Freewater, which is built along its banks, and then flows northward through Milton–Freewater. Irrigation water is drawn from the river here and at numerous locations along the river.