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 (CT), 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.