A study on flood water infiltration and ground water recharge of a shallow alluvial aquifer was conducted in the hyperarid section of the Kuiseb River, Namibia. The study site was selected to represent a typical desert ephemeral river. An instrumental setup allowed, for the first time, continuous monitoring of infiltration during a flood event through the channel bed and the entire vadose zone. The monitoring system included flexible time domain reflectometry probes that were designed to measure the temporal variation in vadose zone water content and instruments to concurrently measure the levels of flood and ground water. A sequence of five individual floods was monitored during the rainy season in early summer 2006. These newly generated data served to elucidate the dynamics of flood water infiltration. Each flood initiated an infiltration event which was expressed in wetting of the vadose zone followed by a measurable rise in the water table. The data enabled a direct calculation of the infiltration fluxes by various independent methods. The floods varied in their stages, peaks, and initial water contents. However, all floods produced very similar flux rates, suggesting that the recharge rates are less affected by the flood stages but rather controlled by flow duration and available aquifer storage under it. Large floods flood the stream channel terraces and promote the larger transmission losses. These, however, make only a negligible contribution to the recharge of the ground water. It is the flood duration within the active streambed, which may increase with flood magnitude that is important to the recharge process.