As part of the JGOFS field program, extensive CO2 partial-pressure measurements were made in the atmosphere and in the surface waters of the equatorial Pacific from 1992 to 1999. For the first time, we are able to determine how processes occurring in the western portion of the equatorial Pacific impact the sea–air fluxes of CO2 in the central and eastern regions. These 8 years of data are compared with the decade of the 1980s. Over this period, surface-water pCO2 data indicate significant seasonal and interannual variations. The largest decreases in fluxes were associated with the 1991–94 and 1997–98 El Niño events. The lower sea–air CO2 fluxes during these two El Niño periods were the result of the combined effects of interconnected large-scale and locally forced physical processes: (1) development of a low-salinity surface cap as part of the formation of the warm pool in the western and central equatorial Pacific, (2) deepening of the thermocline by propagating Kelvin waves in the eastern Pacific, and (3) the weakening of the winds in the eastern half of the basin. These processes serve to reduce pCO2 values in the central and eastern equatorial Pacific towards near-equilibrium values at the height of the warm phase of ENSO. In the western equatorial Pacific there is a small but significant increase in seawater pCO2 during strong El Niño events (i.e., 1982–83 and 1997–98) and little or no change during weak El Niño events (1991–94). The net effect of these interannual variations is a lower-than-normal CO2 flux to the atmosphere from the equatorial Pacific during El Niño. The annual average fluxes indicate that during strong El Niños the release to the atmosphere is 0.2–0.4 Pg C yr-1 compared to 0.8–1.0 Pg C yr-1 during non-El Niño years.