Despite their role in modulating the marine ecosystem, variability and drivers of low‐oxygen events in the offshore northern Benguela Upwelling System (BenUS) have been rarely investigated due to the events' episodicity which is difficult to resolve using shipboard measurements. We address this issue using 4 months of high‐resolution glider data collected between February and June 2018, 100 km offshore at 18°S. We find that oxygen (O2) concentrations in the offshore northern Benguela are determined by the subsurface alternation of low‐oxygen Angola‐derived water and oxygenated water from the south at 100–500 m depth. We observe intermittent hypoxia (O2 < 60 μmol kg−1) which occurs on average for ∼30% of the 4 months deployment and is driven by the time‐varying subsurface pulses of Angola‐derived tropical water. Hypoxic events are rather persistent at depths of 300–450 m, while they are more sporadic and have weekly duration at shallower depths (100–300 m). We find extreme values of hypoxia, with O2 minima of 16 μmol kg−1, associated with an anticyclonic eddy spinning from the undercurrent flowing on the BenUS shelf and showing no surface signature. Fine‐scale patchiness and water mass mixing are associated with cross‐frontal stirring by a large anticyclone recirculating tropical water into the northern BenUS. The dominance of physical drivers and their high variability on short time scales reveal a dynamic coupling between Angola and Benguela, calling for long‐term and high‐resolution measurements and studies focusing on future changes of both tropical O2 minima and lateral fluxes in this region.