The El Niño–Southern Oscillation (ENSO) is a periodic climatic and oceanic event caused by sea-surface temperature and nutrient anomalies over the eastern tropical Pacific Ocean (ETP). Recurring ENSO events have a significant impact on climate and the ecosystems of the circum-Pacific region. In the marine realm, ENSO is known for altering temperature and nutrient patterns, affecting the pelagic food chain, and causing widespread bleaching of corals due to temperature stress. The potential impacts of ENSO on shallow benthic ecosystems as a whole, however, are poorly understood. Here, we compared biogenic sedimentary facies of ETP shallow-water carbonate systems in a strongly ENSO-influenced area (Galápagos Islands, Ecuador [GAL]) with similar systems in an area less strongly influenced by ENSO (Gulf of California, Mexico [GOC]). Carbonate assemblages in both study regions range from coral-algal–dominated (photozoan) to molluscan-dominated (heterozoan) assemblages. Linear statistical models, comparing the distribution of carbonates against prominent local oceanographic parameters, show that minimum chlorophyll-a and maximum sea-surface temperature (which are both strongly influenced by ENSO) are dominant drivers shaping carbonate sediment facies in the GAL. In contrast, GOC carbonates have a distinct mean chlorophyll-a signature that is the result of an upwelling-induced north-south nutrient gradient not significantly influenced by ENSO.