The Sierra Nevada snowpack is vital to the water supply of California, the world’s sixth largest economy. Though tree ring and instrumental records show the dramatic influence of environmental change on California’s hydroclimate over the last millennium, few proxy archives assess winter precipitation variability farther back in time. Here, we use diatoms from a ~3,200 yr. old sediment core to reconstruct the paleolimnology of June Lake, a hydrologically closed glacial lake in the eastern Sierra Nevada. We test the hypothesis that limnologic and climatic changes control diatom assemblages at June Lake. Fossil diatom assemblages from June Lake sediments chiefly consist of the planktic genera Stephanodiscus and Lindavia; their relative abundances in sediments are controlled by lake response to changes in the length of the winter season. We establish a Lindavia:Stephanodiscus index to infer winter length; our results indicate three periods where winter seasons are longer than average: ~3.2-2.9 ka, ~2.2-1.7 ka, and ~0.6 ka-0.05 ka. Over the last ~100 yrs., June Lake has experienced stronger water column stratification and an expansion of the available benthic diatom habitat, indicating significantly warmer winters and lower lake levels. It is possible that this change is the result of anthropogenic climate warming.