The Three Forks Basin sprawls where the intricately deformed sedimentary and volcanic rocks of the Disturbed Belt along the Rocky Mountain front are faulted against the Precambrian metamorphic rocks that make the core of the Tobacco Root, Madison, Gallatin, and Beartooth ranges. Its eastern edge is linear, controlled by steep faults at the west front of the Bridger Range. All other boundaries are sinuous and show little sign of structural control.
Tertiary deposits in the basin, rich in contemporaneous rhyolitic and latitic ash, are about equally of lake, bolson, and stream origin. The western part of the basin is dominated by moderately folded Eocene and lower Oligocene rocks, more than 2000 feet thick. They dip eastward beneath apparently unfolded upper Miocene and Pliocene rocks, more than 1300 feet thick, that also dip gently eastward to the basin edge.
Thin but extensive Quaternary deposits lying unconformably on the Tertiary and pre-Tertiary rocks are mainly of rounded terrace and flood-plain gravel, angular fan gravel, and wind-blown silt.
The basin began as part of an east-flowing stream system that developed in Late Cretaceous and Paleocene time, concurrently with Laramide folding and thrusting; the faulted contact between metamorphic and sedimentary rocks was especially erodible and became a main drainage way. Recurrent uplift to the west throughout the Tertiary provided gradient and load to the streams; additional load was provided by showers of ash from unknown vents. Relative uplifts of the Bridger Range in Eocene and early Oligocene time, and again in late Miocene and Pliocene time, impeded flow from the basin and led to deposits in channels, flood plains, and lakes. During most of Oligocene and Miocene time, however, the basin was being eroded. By the end of the Tertiary the basin was deeply filled and became part of a regional surface of low relief. Regional northwestward tilting stimulated headward erosion of the Missouri River which then captured the formerly east-draining or closed basin. The Tertiary deposits have been deeply eroded, and the rugged pre-basin surface partly exhumed.