Flood-fed aquifers along the sandy lower reach of the Kuiseb River sustain a 130-km-long green belt of lush oases across the hyperarid Namib desert. This oasis is a year-round source for water creating dense-tall woodland along the narrow corridor of the ephemeral river valley, which, in turn, supports human activity and fauna including during the long dry austral winters and multi-year droughts. Occasional floods, originating at the river’s wetter headwaters, travel ∼280 km downstream, before recharging these aquifers. We analyzed the flood-aquifer-vegetation dynamics at-a-site and along the river, determining the relative impact of floods with diverse magnitude and frequency on downstream reaches. We find that flood discharge that feeds the alluvial aquifers also affects vegetation dynamics along the river. The downstream aquifers are fed only by the largest floods that allow the infrequent germination of plants; mean annual recharge volume is too low to support the aquifers level. These short-term vegetation cycles of green-up and then fast senescence in-between floods are easily detected by satellite-derived vegetation index. This index identifies historical floods and their magnitudes in arid and hyperarid regions; specifically, it determines occurrences of large floods in headwater-fed, ephemeral Namib streams as well as in other hyperarid regions. Our study reveals the importance of flood properties on the oasis life cycle, emphasizing the impact of drought and wet years on the Namib’s riparian vegetation.