Satellite observations show that large-scale phytoplankton blooms (increases in chlorophyll) occurred in the equatorial Pacific in 1998, 2003, and 2005, following termination of the three most recent El Ni¿o events. The occurrence of blooms following successive El Ni¿o events cannot be explained by local enhancement of vertical nutrient flux, as evidenced by observations of equatorial winds, thermocline depth, and the depth and strength of the Equatorial Undercurrent (EUC, which supplies the limiting nutrient iron to the euphotic zone). However, near the peak of each El Ni¿o event (late in 1997, 2002, and 2004), while the thermocline of the western equatorial Pacific was anomalously shallow, the flow of the New Guinea Coastal Undercurrent (NGCUC, which is the primary source of iron-enriched waters to the EUC) intensified, and its core shoaled from >200 m to ~100 m depth. Analysis of NGCUC variability using a high-resolution, terrain-following three-dimensional ocean circulation model simulation indicates that as the NGCUC shoals and intensifies, it develops meanders and eddies that augment coupling of the New Guinea shelf and upper slope to the EUC. We hypothesize that these changes in NGCUC circulation during El Ni¿o enhance iron transport from the New Guinea margin into the EUC and thereby trigger large-scale blooms when iron-enriched waters subsequently reach the euphotic zone along the equator. The threefold to fourfold chlorophyll increases over large regions, up to ~5 ¿ 105 km2, must have profound impacts on the equatorial ecosystem and biogeochemical cycles.