Its headwaters are in Clackamas County, in the Table Rock Wilderness Area, near Table Rock, in the Cascade Range. After descending from the mountains, it becomes a slow meandering stream, passing through a fertile agricultural region of the lower Willamette Valley.
It is joined by the Pudding shortly before flowing into the Willamette near the town of Canby. The confluence of the Molalla, Pudding, and Willamette form a floodplain that provides one of the most significant habitats for small mammals and waterfowl in the Willamette Valley, including the largest blue heron rookery in the region.
During the early 1800's, the area around the river was populated by the Molalla Indians. During that time, an extensive system of trails along the river allowed trade being the peoples of the Willamette Valley and eastern Oregon. As late as the 1920's, the trails were used by Native Americans from the Warm Springs Indian Reservation to reach huckleberry-picking grounds near Table Rock [1] . One of the original routes, called the "Huckleberry Trail", is currently used for recreational hiking and horseback riding.
Starting in the 1840's, the lower Molalla became an area of intense homesteading by European-Americans because of the fertility of the surrounding land. The upper reaches of the river became an area of widespread logging, as well as gold mining near the head of Ogle Creek.