The Jefferson basin trends northward, elongated parallel to the southeastern border of the Boulder batholith on the west, and the linear fault-controlled flanks of the Tobacco Root and Bull Mountain areas on the east. The otherwise linear eastern margin of the basin is interrupted by an embayment that extends eastward between the Tobacco Root and Bull Mountain areas to coincide with the projected westward trace of the ancient Willow Creek fault zone in the Three Forks basin.

Continental Tertiary basin-fill deposits of fluvial, lacustrine, and eolian origin (Bozeman Group, Robinson, 1963) overlie pre-basin rocks with erosional and angular unconformity. The Bozeman Group, represented by two unconformable and lithologically distinct depositional sequences is subdivided into two formations: the Renova Formation (new name), 0 to 3,500 + ft thick, partly of early and middle Oligocene age; and the Sixmile Creek Formation (Robinson, 1967), 0 to 2,400 + ft thick, of late Miocene to middle Pliocene age. The Renova Formation, characterized by fine-grained strata deposited in low-energy flood plain and pond environments, is subdivided into: the Bone Basin Member (new name), predominantly interbedded micrite and montmorillonite mudstone; the Climbing Arrow Member, predominantly montmorillonite mudstone; and the Dunbar Creek Member, predominantly vitric siltstone. The Sixmile Creek Formation, characterized by coarse-grained strata which accumulated in relatively high-energy ephemeral and perennial channel environments, is typified by locally derived fanglomerate near the basin margin; and by pebbly arkose, vitric arenite, and subordinate rounded conglomerate in more central parts of the basin.

Renova strata along the western margin of the basin dip eastward from unconformable contacts with pre-basin rocks and disappear beneath gently dipping Pliocene Sixmile Creek strata in the central part of the basin. North of the Tobacco Root Mountains, Renova strata repeated by displacement along the Tobacco Root fault, are moderately folded and faulted and overlain by tilted Miocene and Pliocene Sixmile Creek strata, that dip eastward into the Mayflower Gulch fault. Both Renova and Six-mile Creek strata are unconformably overlain by thin Quaternary deposits of diverse origin.

The Jefferson basin had its beginning when east-west and north-south zones of weakness produced by Laramide faulting were eroded subsequently by an eastward-flowing drainage system to produce an irregular erosion surface cut sufficiently deep to expose the Boulder batholith. By the Oligocene, drainage was impaired and lower and middle Oligocene Renova Formation strata were deposited and subsequently folded probably by adjustment along buried faults. Post-Renova erosion removed a large volume of Renova strata before the oldest Sixmile Creek strata accumulated in the late Miocene. Sixmile Creek strata continued to accumulate until the late Pliocene when a new cycle of basin excavation was initiated. During basin excavation, but before the late Pleistocene, displacement along the Tobacco Root fault raised the Bull Mountain and Tobacco Root Mountain blocks relative to the basin area to the west. The Tobacco Root block was independently rotated eastward, probably by concurrent faulting along the Mayflower Gulch and Jefferson faults, tilting Renova and Sixmile Creek strata at the north end of the Tobacco Root Mountains eastward. Following deformation, continued excavation of the basin left Renova and Sixmile Creek strata deeply eroded and the irregular pre-basin erosion surface partly exhumed.

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