Genovesa Crater Lake is a remote, hyper-saline lake in the northern Galápagos archipelago that contains a finely laminated sediment record. This sediment record has the potential to provide a high-resolution history of past climate variability in the eastern tropical Pacific. Here we present modern climate, lake, and sediment observations from 2009 to 2012 to explore how local climate variability influences Genovesa Crater Lake and its sediments. Surface lake temperature is strongly linked to air temperature and is highly seasonal. Temperature stratification is strongest during the warm season, whereas temperature becomes more uniform through the water column in the cool season. Deeper and earlier mixing occurred during the 2010 La Niña , which subsequently delayed 2011 cool season mixing and maximum warm season surface temperatures in 2011 and 2012. Lake salinity changes are influenced by precipitation, evaporation and persistent seawater influx. The largest declines in subsurface salinity follow months after the rainy season, when temperatures cool and fresher surface water from the previous warm/wet season mixes into the subsurface. Between 2009 and 2012, more calcium carbonate precipitated during a period of higher salinity. The period of highest calcium carbonate abundance measured in sediment records that span the late nineteenth to twentieth century coincides with the failure of two Electronic supplementary material The online version of this article (doi:10.1007/s10933-014-9797-z) contains supplementary material, which is available to authorized users.