During a strong El Niño event, nutrient and phytoplankton concentrations around the Galapagos archipelago greatly decrease, while sea surface temperature increases (>7°C). Several species suffer under these conditions, while some benefit and new species appear. To understand the mechanisms behind observed changes, a trophic reference model of the Bolivar Channel ecosystem was forced by a 16 yr (1994 to 2009) satellite-derived time series of phytoplankton biomass including the El Niño period 1997/98. Emergent changes in model compartment biomasses, as derived from dynamic simulations, were compared to in situ observations of the subtidal communities and marine vertebrates over the study period. Observed population reductions of seabirds (penguins and flightless cormorants) and of several fish groups were well predicted by the simulations, suggesting that bottom-up effects largely control the system during an El Niño event. Observational data also enabled modifying the reference model to an El Niño state model. In this El Niño model, ecosystem size (total energy throughput) was reduced by 70.1%. Overall system characteristics show great similarities with other coastal upwelling systems of the Peruvian coast in that strong El Niño events cause disruptions to trophic flows and keep them at a low (but highly productive) development state.