Finely laminated sediments within Bainbridge Crater Lake, Galápagos provide a record of El Niño-Southern Oscillation (ENSO) events over the Holocene. Despite the importance of this sediment record, hypotheses for how climate variability is preserved in the lake sediments have not been tested. Here we present results of long-term monitoring of the local climate and limnology and a revised interpretation of the sediment record. Brown-green, organic rich, siliciclastic laminae reflect warm, wet conditions typical of El Niño events, whereas carbonate and gypsum precipitate during cool, dry La Niña events and persistent dry periods, respectively. Applying this new interpretation, we find ENSO events of both phases were generally less frequent during the mid-Holocene (~6100-4000 cal. years BP) relative to the last ~1500 cal. years. Abundant carbonate laminations between 3500 and 3000 cal. years BP imply that conditions in the Galápagos region were cool and dry during this period when the tropical Pacific E-W SST gradient likely strengthened. The frequency of El Niño and La Niña events then intensified dramatically around 1750-2000 cal. years BP, consistent with a weaker SST gradient and an increased frequency of ENSO events in other regional records. This strong interannual variability persisted until ~700 cal. years BP, when ENSO-related variability at the lake decreased as the SST gradient strengthened. Persistent, dry conditions then dominated between 300 and 50 cal. years BP (AD 1650-1900, ± ~100 years), whereas wetter conditions and frequent El Niño events dominated in the most recent century.