El Niño has profound influences on ecosystem dynamics. However, we know little about how it shapes vertebrate faunal community composition over centennial time scales, and this limits our ability to forecast change under projections of future El Niño events. On the basis of correlations between geological records of past El Niño frequency and the species composition of bird and fish remains from a Baja California bone deposit that spans the past 12,000 years, we documented marked faunal restructuring when major El Niño events occurred more than five times per century. This tipping point has implications for the past and future ecology of eastern Pacific coastal environments.