Net ecosystem production (NEP) rates of dissolved organic carbon (DOC) are estimated in a coastal upwelling system. The study site is a large coastal inlet (2.76 km3) in the northern boundary (42–43°N) of the eastern North Atlantic upwelling system. The two‐dimensional circulation pattern in the system is governed by an offshore Ekman transport quite variable in magnitude and direction. A mass balance of the short‐timescale (2–4 d) changes in measured DOC profiles is performed to obtain the NEP rates. Microbial oxidation of imported labile DOC (8% of total DOC, recycling time t < 5 d) at a maximum net rate of −37 mmol C m−2 d−1 occurred during a downwelling episode in the middle of the highly productive spring period. On the contrary, extensive export of labile DOC (<15% of total DOC, t < 7 days) produced at net rates >42 mmol C m‐2 d‐1 took place during an upwelling episode in July, the middle of the upwelling season. This rate represents ~20% of the net primary production, demonstrating in the field the relative importance of horizontal offshore transport of labile DOC to the export of new production in upwelling systems. An autumn wind relaxation period results in dramatic changes in DOC standing stocks (69 mmol C L‐1) caused by a conspicuous time segregation between sustained net phytoplankton production of labile DOC (+15 mmol C m‐2 d‐1, 11 d) and subsequent rapid bacterial degradation (−63 mmol C m‐2 d‐1, 3 d). Net horizontal export during this period was prevented by reduced offshore Ekman transport values, indicating that net DOC production is not always synonymous with net export. Finally, during the winter period, the large wind‐driven net DOC horizontal exchange rates affected mainly the DOC standing stocks of no bioreactive materials in the system, whereas bacterial oxidation rates during this period reduced to less than −0.14 mmol C m‐2 d‐1.