The Flagstaff Limestone of Paleocene and early Eocene age, and coeval rocks of the North Horn and Colton Formations of central Utah, were deposited in the Lake Flagstaff lacustrine-alluvial complex. The Flagstaff lake basin formed in response to postorogenic deformation along the Sevier thrust belt and Laramide basement uplifts that blocked drainage. The Flagstaff Limestone of the Wasatch Plateau consists of three members; the lower member, designated Ferron Mountain, and the upper, the Musinia Peak, represent major high stands of the lake. They consist of mudstone, brecciated and massive carbonate rock with rootlets and pedogenic features, laminated and structureless limestone, fossiliferous limestone, and oncolitic and sandy limestone. During deposition of the Ferron Mountain Member, the eastern margin of the lake was vegetated, very shallow, and episodically exposed. In contrast, a relatively steep, high-energy shoreline along active structural elements bounded the west side of the lake. The middle member, designated Cove Mountain, consists of mud-cracked dolomicrite, mudstone, and bedded and nodular gypsum. These beds reflect repeated contractions and expansions of the lake across a broad carbonate mud flat. Freshwater limestones that were deposited during expansions of the lake probably were altered to dolomicrite during contractions by evaporative pumping of brine on mud flats.

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