The southern Taos Valley encompasses the physiographic and geologic transition zone between the Picuris Mountains and the San Luis Basin of the Rio Grande rift. The Embudo fault zone is the rift transfer structure that has accommodated the kinematic disparities between the San Luis Basin and the Española Basin during Neogene rift extension. The eastern terminus of the transfer zone coincides with the intersection of four major fault zones (Embudo, Sangre de Cristo, Los Cordovas, and Picuris-Pecos), resulting in an area of extreme geologic and hydrogeologic complexities in both the basin-fill deposits and the bedrock. Although sections of the Embudo fault zone are locally exposed in the bedrock of the Picuris Mountains and in the late Cenozoic sedimentary units along the top of the Picuris piedmont, the full proportions of the fault zone have remained elusive due to a pervasive cover of Quaternary surficial deposits. We combined insights derived from the latest geologic mapping of the area with deep borehole data and high-resolution aeromagnetic and gravity models to develop a detailed stratigraphic/structural model of the rift basin in the southern Taos Valley area. The four fault systems in the study area overlap in various ways in time and space. Our geologic model states that the Picuris-Pecos fault system exists in the basement rocks (Picuris formation and older units) of the rift, where it is progressively down dropped and offset to the west by each Embudo fault strand between the Picuris Mountains and the Rio Pueblo de Taos. In this model, the Miranda graben exists in the subsurface as a series of offset basement blocks between the Ponce de Leon neighborhood and the Rio Pueblo de Taos. In the study area, the Embudo faults are pervasive structures between the Picuris Mountains and the Rio Pueblo de Taos, affecting all geologic units that are older than the Quaternary surficial deposits. The Los Cordovas faults are thought to represent the late Tertiary to Quaternary reactivation of the old and deeply buried Picuris-Pecos faults. If so, then the Los Cordovas structures may extend southward under the Picuris piedmont, where they form growth faults as they merge downward into the Picuris-Pecos bedrock faults. The exceptionally high density of cross-cutting faults in the study area has severely disrupted the stratigraphy of the Picuris formation and the Santa Fe Group. The Picuris formation exists at the surface in the Miranda and Rio Grande del Rancho grabens, and locally along the top of the Picuris piedmont. In the subsurface, it deepens rapidly from the mountain front into the rift basin. In a similar manner, the Tesuque and Chamita Formations are shallowly exposed close to the mountain front, but are down dropped into the basin along the Embudo faults. The Ojo Caliente Sandstone Member of the Tesuque Formation appears to be thickest in the northwestern study area, and thins toward the south and the east. In the study area, the Lama formation thins westward and southward. The Servilleta Basalt is generally thickest to the north and northwest, thins under the Picuris piedmont, and terminates along a major, linear, buried strand of the Embudo fault zone, demonstrating that the Servilleta flows were spatially and temporally related to Embudo fault activity.