The Swakop River is a major ephemeral river (drainage basin area about 30,000 km²) crossing the western Namib Desert. Its hydrology and limited water resources depend on storms and floods. Therefore, the hydrology and flow regime in the Swakop River basin determines the availability of water for human use. In this study we present a millennia-long record of extreme floods, using paleoflood hydrological methods and optically stimulated luminescence (OSL) ages. The record includes 44 large floods ranging in date from the late Pleistocene to the present. The oldest six to eight floods are dated from the late Pleistocene to the mid-Holocene (between 14,900 ± 1700 and 5100 ± 620 years ago), with calculated peak discharges of 550–1280 m³ s⁻¹. Eighteen floods, eleven of which were between 1000 and 1600 m³ s⁻¹, occurred between 740 ± 90 and 190 ± 10 years ago. Additional 17 later floods occurred between about AD 1850 and 1963, with peak discharges between 100 and 1000 m³ s⁻¹. The historical record which partly parallels the latter period recorded 17 large floods during the period 1893–1963. Flood frequency analysis (FFA) of the combined systematically gaged record (1963–2003) and the paleoflood record since AD 1270 (740 ± 90 years, the most complete record), was applied using the maximum likelihood method. A two-component extreme value distribution (TCEV) estimates the 1% annual exceedance probability magnitude, using only the systematic gaged record at 520 m³ s⁻¹. The combined paleoflood, historical, and gage records resulted in a much larger magnitudes for the 1% annual exceedance probability flood magnitude of 1320–1350 m³ s⁻¹. The 0.1% annual exceedance probability magnitude is estimated at 770 m³ s⁻¹ and 2100–2150 m³ s⁻¹, respectively. The hydroclimatic interpretation of this paleoflood record is complex, due to the discontinuity of the record. During the late Holocene, our flood data show three intervals differing in their flood regime: (1) 1280 ± 80 to 740 ± 90 years BP, with one extraordinary flood (>200 m³ s⁻¹) about every 180 years; (2) 740 ± 90 to 200 ± 45 ¹⁴C years BP, with one large flood per 80 years; and (3) 200 ± 45 ¹⁴C years BP to AD1963, with one large flood per 7 years. Interval 2 represents large floods, probably related to the transition from a drier climate to the colder and probably wetter climate of the Little Ice Age (LIA). The third period relates to the end of the LIA and to a wetter period of the 19th and early 20th centuries in which more rainfall in the Kalahari and Namib Deserts and many historical floods were documented. The presence of three distinct calcretes rich in calcified rhizoliths at one of the sites, two of which were dated by OSL to 13.2 ± 1.9 ka and 8.8 ± 1.0 ka, indicates, at least locally, higher moisture availability than in the current semiarid climate; the presence of denser vegetation can be associated with increased groundwater seepage and wetter climatic conditions. Keywords: Namib Desert, Paleofloods, OSL, Paleoclimate, Swakop River, Flood frequency.