Interpretation of gravity, magnetotelluric, and aeromagnetic data in conjunction with geologic constraints reveals details of basin geometry, thickness, and spatiotemporal evolution of the southern San Luis Basin, one of the major basins of the northern Rio Grande rift. Spatial variations of low-density basin-fill thickness are estimated primarily using a 3D gravity inversion method that improves on previous modeling efforts by separating the effects of the low-density basin fill from the effects of pre-rift rocks. The basin is found to be significantly narrower—and more complex in the subsurface—than indicated or implied by previous modeling efforts. The basin is also estimated to be significantly shallower than previously estimated. Five distinct subbasins are recognized within the broader southern San Luis Basin. The oldest and shallowest subbasin is the Las Mesitas graben along the northwestern basin margin, formed during the Oligocene transition from Southern Rocky Mountain volcanic field magmatism to rifting. In this subbasin, sediments are estimated to reach a maximum thickness of ~400 m within a north–south elongated structural depression. Other subbasins that likely initially developed during the Miocene are the dominant tectonic features in the southern San Luis Basin. This includes the Tres Orejas subbasin, which formed in the southwestern portion of the basin by the Embudo fault zone and a hypothesized fault zone along its western margin. This subbasin reaches a maximum thickness of ~2 km, as indicated by magnetotelluric and gravity modeling. The Sunshine Valley, Questa, and Taos subbasins occupy the eastern part of the southern San Luis Basin. The southern Sangre de Cristo fault zone is the dominant tectonic feature that controlled their development after ~20 Ma. The east-down Gorge fault zone controlled the western margins of significant parts of these eastern subbasins, although much of the Taos subbasin may be superimposed on the Tres Orejas subbasin. Maximum low-density basin-fill thicknesses are estimated to be 1.2 km for the Sunshine Valley subbasin, 800 m for the Questa subbasin, and 1.8 km for the Taos subbasin. Subbasin-forming tectonic activity along the Gorge fault zone and within the Tres Orejas subbasin ceased by the end of the development of the largely Pliocene Taos Plateau volcanic field. After that, rift-related subsidence became more narrowly centered on the eastern margin of the basin, controlled mainly by the linked Embudo and southern Sangre de Cristo fault zones.