Mission Canyon deposition occurred in southwest Montana on a shallow carbonate platform that extended to the Antler orogenic foreland basin, the eastern margin of which is near the Idaho-Montana border. Deposition on this platform did not take place in regular facies belts paralleling depositional strike, but instead occurred on fairly regular shelves (Alberta and Beartooth) in the east, and along shoals, emergent islands, and deeper water channels throughout most of the area. The facies that were deposited in these zones are directly related to the northeast-southwest and northwest-southeast structural trend imposed on the area during late Precambrian time, and the movement of paleostructural elements during Mission Canyon and pre-Big Snowy time. The thickest sequences i the Mission Canyon are those comprised of low-energy mudstones and wackestones, which were deposited in trough areas such as the Ruby and Centennial troughs, and the high to moderate-energy grainstone and packstone sections that typify the far western shelf margin sequences.

High-energy shoal (lime grainstone) and low-energy island (algal boundstone) deposits are concentrated both on and around fault-bounded paleohighs (e.g., Pioneer Mountains in the Belt Island Complex) present during early Mission Canyon time; they are represented by thins on the Mission Canyon isopach map. Paleolows, such as the Ruby-Crazy Mountain and Centennial troughs, developed on east-northeast-trending, downdropped, fault-bounded basement blocks, and were filled with thick sequences of mostly restricted marine dolomite mudstones and wackestones. These restricted marine lithologies also occur as relatively thin zones in the upper portions of the fining upward high-energy shoal sequences in the lower Mission Canyon. However, they are most extensively developed in the upper Mission anyon, where they contain regionally correlative evaporite units that are represented on outcrop by solution collapse breccias. Only minor amounts of low energy, normal marine rocks occur in the Mission Canyon Formation, and most of these were deposited near the far western margins of the carbonate platform.

A major lowering of sea level took place in middle Mission Canyon time. This resulted in the deposition of a regionally correlative supratidal sequence. The ensuing regional transgression resulted in the development of a new shelf margin farther to the west, and deposition of the restricted marine and evaporite units, mentioned above, behind it. Deposition of the Mission Canyon Formation ended with the total withdrawal of the sea from southwest Montana, regional exposure, and the formation of an extensive karst system and widespread solution collapse breccias.

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