The Santa Cruz arroyo in the Tucson Basin, Arizona, has undergone major environmental changes over the last 8000 years. The Holocene stratigraphy along a 15-km segment of the arroyo, known as the San Xavier reach, which traverses the San Xavier Indian Reservation was investigated in detail. The Holocene alluvial sequence reveals that aggradation occurred until 8000 yr BP within a braided stream, was followed by a major period of channel erosion and widening from 8000 to 5500 yr BP, which, in turn, was followed by vertical aggradation of the floodplain and five short periods of channel cutting. Broad climatic changes are correlated with major changes in the fluvial regime and landscape. However, the cycles of arroyo cutting and filling, during the semiarid climate of the last 2500 years, were probably the result of the creation of unstable internal geomorphic conditions, flooding, and human impacts on the floodplain. The alluvial history of the San Xavier reach has had a pronounced effect on the preservation and completeness of the archaeological record. Periods of erosion have created absences or gaps in the archaeological record and deep burial has removed some of the preserved archaeological remains from view. Environment changes on the floodplain also influenced late prehistoric Hohokam settlement and subsistence patterns in the San Xavier region.