Emerging understanding of the variability of natural coastal hypoxia is divided between two main hypotheses: the biogeochemical oxygen demand linked to locally-driven organic matter decay or to supply of low-oxygen waters by physical processes. The precise role of either mechanism in triggering hypoxia has remained elusive. A combined methane and oxygen high resolution year-long hourly data time series in a coastal upwelling system suggests that these systems may be responding to a complex interaction between the two. The data show how anoxia is initially triggered by remote equatorial hypoxic waters after which it can be sustained by a local biogeochemical flux of exported production. Crucially, without a remote trigger the local forcing could not develop anoxic conditions because the physical flux of oxygen would be too high. The robustness of this interpretation is tested using a 10-year data set (1994–2003) with seasonal and interannual scales of variability.