Under physically isolated conditions, net community production (NCP) can be accurately estimated from the rate of oxygen evasion to the atmosphere derived from local mixed layer oxygen/argon measurements. We use a simple box model to demonstrate that, when physical inputs are negligible, the sea‐to‐air flux of biological oxygen (bioflux) represents the average NCP exponentially weighted over the past several residence times of oxygen in the mixed layer. This new weighting scheme shows that there is no apparent lag between bioflux and exponentially weighted time‐averaged NCP. Furthermore, a strict steady state assumption is unnecessary to this relationship. However, this widely used O2/Ar method is not effective in dynamic coastal zones where low oxygen water upwells to the surface. Yet these zones are highly productive and their episodic productivity needs to be quantified. We use a quasi‐2‐D version of the Regional Ocean Modeling System, including oxygen and argon as prognostic variables, to explore the application of this method and the relationship between NCP and bioflux in a coastal upwelling system. We show that bioflux is an accurate measure of NCP over large regions of time and space. Bioflux is most biased near the shore following upwelling favorable winds, where bioflux is sometimes negative (flux from the atmosphere to the ocean) and even positive bioflux values can severely underestimate NCP. Assessing a range of model variables that are easily observed in the field, we show that sea surface temperature is the most effective at identifying bioflux measurements that are likely to be biased.
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