Paleoclimate records from the tropical Pacific suggest the early to mid-Holocene was a period of reduced El Niño/Southern Oscillation (ENSO) variability, with a transition to modern, increased ENSO frequency occurring some time in the last few thousand years. However, the nature and timing of this shift remains uncertain due to the discontinuous nature and/or coarse resolution of many ENSO proxies, as well as a lack of agreement between previously published records. A new, continuous, climate record from El Junco Crater Lake in the Galápagos Islands reveals several abrupt changes in lake level and precipitation through the Holocene. Hydroclimatic model simulations suggest that El Junco lake level responds sensitively to increases in precipitation associated with El Niño events, rising during wet El Niño events and falling during the intervening dry periods. Grain size data from El Junco sediment cores indicate past lake level variability, likely associated with changing seasonal precipitation and ENSO frequency. The grain size data suggest increased precipitation intensity prior to 9000±120 cal years BP, and after 4200±130 cal years BP, as well as a two-step increase in precipitation at 3200±160 and 2000±100 cal years BP. Maximum Holocene precipitation and inferred ENSO variability occurred between 2000±100 and 1500±70 cal years BP, during the same period that six other independent proxy records suggest higher ENSO frequency and longer, stronger El Niño events. Decreasing sediment carbon/nitrogen (C/N) ratios in El Junco sediments indicate rising lake levels from the early Holocene to present, corroborating the grain size data. The inferred increase in precipitation at 4200±130 cal years BP and at 2000±100 cal years BP coincides with decreasing Southwest Asian and East Asian Monsoon intensity, suggesting tropical Pacific climate and the Asian monsoon were interconnected systems at centennial to millennial timescales during the Holocene. A weakening trend in the Asian monsoon and the trend toward wetter conditions at El Junco also coincide with a trend toward cooler and drier conditions inferred from Cariaco Basin sediment proxies from the mid-Holocene to present, suggesting the migration of the Intertropical Convergence Zone (ITCZ) likely influenced hydrological changes in both the eastern tropical Pacific and the Asian Monsoon region during the Holocene.