A numerical model is used to quantify the pathways of carbon flow through the planktonic ecosystem from 1996 through 1998 at 9.5°S off the coast of Peru. The objective was to evaluate the response of the planktonic ecosystem to the forcing associated with normal conditions in 1996, the 1997–1998 El Niño, and the La Niña which began in June of 1998. During El Niño, the depth of the upper layer increased, temperature increased, and the nitrate concentration in the source water for upwelling was reduced. La Niña forcing was the opposite. The simulated phytoplankton biomass, carbon uptake, vertical export, and food available for higher trophic levels were reduced during the El Niño period compared to normal conditions. Phytoplankton biomass and uptake were slightly less during La Niña than in 1996, though carbon export and advective loss were significantly enhanced. A series of numerical experiments were run to determine whether the upwelling rate, source water characteristics, depth of the upper layer, or phytoplankton size composition of the source water was the primary forcing factor for the planktonic community. Although all factors contributed to the magnitude of the simulated response, the primary determinant for El Niño conditions was the concentration of new nitrogen in the upwelling source water, followed by depth of the upper layer and upwelling rate. The depth of the upper layer was the dominant forcing term for La Niña, followed by upwelling rate and temperature of the source water.