The 1997–1998 El Niño generated large floods throughout southern Peru, especially in inland locations along Rio Moquegua. Using remote sensing, hydraulic modeling, field surveying, and stratigraphic analyses, we estimate the magnitude and frequency of this flood and determine a late Holocene flood history for main- stem and tributary sections. Modeling indicates a peak discharge of 450 m3/s for the 1998 flood, with an estimated recurrence interval between 50 and 100 yr. Flood deposits for two large events, dated to A.D. 690 and A.D. 1300, respectively, exist in a small tributary system. Tiwanaku site abandonment (ca. A.D. 1000) predates the younger flood, indicating that stratigraphically recognizable El Niño–driven floods were not a causal mechanism for abandonment. Although possessing three flood units, main-stem alluvium is considerably younger (<320 14C yr B.P.) than tributary alluvium, evidencing the major channel widening and lateral reworking of the main stem.