Lake sediment cores contain useful archives of severe past climate events (e.g. droughts, hurricanes, dust storms) and patterns of global climate change. Most such records come from higher latitudes in the Northern Hemisphere. Here we present sediment core data from shallow, equatorial Lake La Tembladera on the southern coast of Ecuador, which contains a > 100-year record of flooding events. We used geochemical properties of a 210Pb-dated sediment core to identify two distinct sedimentary facies. Facies one represents lake-derived deposits and is characterized by sediments with relatively higher organic matter and nitrogen content. Facies two represents flood events and is characterized by sediments with greater concentrations of inorganic carbon and terrigenous elements Al and Ti. Pollen from introduced Pinus sp. and Hg associated with recent gold mining provided independent time-markers in the sediment to validate the 210Pb chronology. The comparisons of the geochemical signal with the ENSO reconstructions revealed that the sediments contain a poor signal of ENSO from AD 1930–1965. The weak ENSO signal may result from minimal climate sensitivity in the lake or early water control efforts (e.g. rudimentary damming). However, from AD 1965, the climate signal is totally masked by recent and documented anthropogenic works such as dams and canals. This record shows how anthropogenic efforts to minimize societal impacts of ENSO floods have masked the natural climate signal and nicely mirrored recent trends between climate and anthropogenic activities in tropical latitudes.