The Upper Devonian Ignacio Formation (as stratigraphically revised) comprises a transgressive, tide-dominated estuarine depositional system in the San Juan Mountains (Colorado, USA). The unit backfills at least three bedrock paleovalleys (10–30 km wide and ≥42 m deep) with a consistent stratigraphy of tidally influenced fluvial, bayhead-delta, central estuarine-basin, mixed tidal-flat, and estuarine-mouth tidal sandbar deposits. Paleovalleys were oriented northwest while longshore transport was to the north. The deposits represent Upper Devonian lowstand and transgressive systems tracts. The overlying Upper Devonian Elbert Formation (upper member) consists of geographically extensive tidal-flat deposits and is interpreted as mixed siliciclastic-carbonate bay-fill facies that represents an early highstand systems tract. Stratigraphic revision of the Ignacio Formation includes reassigning the basal conglomerate to the East Lime Creek Conglomerate, recognizing an unconformity separating these two units, and incorporating strata previously mapped as the McCracken Sandstone Member (Elbert Formation) into the Ignacio Formation. The Ignacio Formation was previously interpreted as Cambrian, but evidence that it is Devonian includes reexamined fossil data and detrital zircon U-Pb geochronology. The Ignacio Formation has a stratigraphic trend of detrital zircon ages shifting from a single ca. 1.7 Ga age peak to bimodal ca. 1.4 Ga and ca. 1.7 Ga age peaks, which represents local source-area unroofing history. Specifically, the upper plate of a Proterozoic thrust system (ca. 1.7 Ga Twilight Gneiss) was eroded prior to exposure of the lower plate (ca. 1.4 Ga Uncompahgre Formation). These results are a significant alternative interpretation of the geologic history of the southern Rocky Mountains.