The 15-km segment of the Santa Cruz River, traversing the San Xavier Indian Reservation, near Tucson, Arizona, has undergone major environmental changes during the past 8,000 yr. The Holocene alluvial sequence for this segment, called the "San Xavier reach" of the Santa Cruz River, shows three major episodes: aggradation until 8000 yr B.P. by a braided stream; channel erosion from 8000 to 5500 yr B.P.; and subsequent vertical aggradation of the flood plain, punctuated by short periods of arroyo cutting. The major changes in the fluvial regime were probably the result of climatic changes, but cycles of arroyo cutting and filling during the past 2,500 yr were probably the result of unstable internal geomorphic conditions, flooding, and human impacts on the flood plain. The alluvial history of the San Xavier reach had a pronounced effect on the preservation of archaeological remains. Environmental changes on the flood plain, including arroyo cutting and filling, cienega formation and destruction, and sand-dune development, led to the disruption and reorganization of Hohokam settlement and subsistence patterns between 1150 and 500 yr B.P.