Variations in rock magnetic properties are responsible for the many linear, short-wavelength, low-amplitude magnetic anomalies that are spatially associated with faults that cut Neogene basin sediments in the Rio Grande rift, including the San Ysidro normal fault, which is well exposed in the northern part of the Albuquerque Basin. Magnetic-susceptibility measurements from 310 sites distributed through a 1200-m-thick composite section of rift-filling sediments of the Santa Fe Group and prerift Eocene and Cretaceous sedimentary rocks document large variations of magnetic properties juxtaposed by the San Ysidro fault. Mean volume magnetic susceptibilities generally increase upsection through eight map units: from 1.7 to 2.2E-4 in the prerift Eocene and Cretaceous rocks to 9.9E-4–1.2E-3 in three members of the Miocene Zia Formation of the Santa Fe Group to 1.5E-3–3.5E-3 in three members of the Miocene–Pleistocene Arroyo Ojito Formation of the Santa Fe Group. Rock magnetic measurements and petrography indicate that the amount of detrital magnetite and its variable oxidation to maghemite and hematite within the Santa Fe Group sediments are the predominant controls of their magnetic property variations. Magnetic susceptibility increases progressively with sediment grain size within the members of the Arroyo Ojito Formation (deposited in fluvial environments) but within members of the Zia Formation (deposited in mostly eolian environments) reaches highest values in fine to medium sands. Partial oxidation of detrital magnetite is spatially associated with calcite cementation in the Santa Fe Group. Both oxidation and cementation probably reflect past flow of groundwater through permeable zones. Magnetic models for geologic cross sections that incorporate mean magnetic susceptibilities for the different stratigraphic units mimic the aeromagnetic profiles across the San Ysidro fault and demonstrate that the stratigraphic level of dominant magnetic contrast changes with different exposure levels into the fault. These data indicate that tectonic juxtaposition of primary variations of magnetic properties of strata across the fault is the source of the associated magnetic anomaly. This study indicates that magnetic anomalies over faults and folds can be generated by sediments (1) deposited within tectonic basins having volcanic or basement source areas rich in magnetite, (2) having depositional environments with sufficient but varying energy to transport dense magnetic minerals and cause stratigraphic changes of magnetic properties, and (3) having magnetic minerals preserved owing to their youth or nonreactive geochemical environments.