Carbonate system parameters were measured in the upper 200 m of the water column during July 1997 in an upwelling area off northern Chile (22.6°–24°S), and the CO₂ fluxes were estimated. At this time (during the onset of El Niño 1997–1998), the water column that feeds the coastal upwelling was less dense, warmer, and saltier than in non-El Niño winters. Nevertheless, the major vertical gradients in pH, total inorganic carbon (C_T), carbon dioxide fugacity (fCO₂), and apparent oxygen utilization (AOU) remained confined to the upper 100 m of the water column, so that the active upwelling forced by southerly winds caused the upwelling of CO₂-rich water leading a CO₂ flux from the ocean to the atmosphere. However, these fluxes were found to be highly variable. Grid surveys 2 weeks apart show a change in CO₂ flux from +3.9 mol C m⁻² yr⁻¹ to +0.4 mol C m⁻² yr⁻¹: the change is thought to be associated with a pulsed upwelling forcing in combination with an active biological uptake of CO₂. This high short-term variability of CO₂ fluxes makes it difficult to assess the interannual variability of CO₂ outgassing in this area based on low-frequency direct CO₂ observations. The fact that the oxycline, whose location usually coincides with the carboncline, also remained within the upper 100 m during the remarkably warm 1972 and 1983 El Niño winters seems to imply that the CO₂ outgassing during those warm periods can be as strong as we report for 1997 under similar upwelling favorable winds.