As historic drought conditions become more common in western North America, Late Quaternary hydroclimate records become vital for putting present anthropogenic conditions into a longer-term context. Here, we establish a high-resolution record of drought for the eastern Sierra Nevada (California) using lacustrine carbonates from well-dated sediment cores. We used oxygen and carbon stable-isotope ratios, combined with high-resolution scanning X-ray fluorescence counts of calcium (Ca) and titanium (Ti), to reconstruct the drought record over the last 4600 years in June Lake. We found elevated δ18O and δ13C carbonate isotope values coinciding with peaks in both total inorganic carbon and Ca/Ti, suggesting enhanced carbonate precipitation in response to evaporative concentration of lake water. At least six intervals of prolonged (centennial-scale) carbonate deposition were identified, including three pulses during the Late Holocene Dry Period (LHDP; ~3500–2000 cal yr BP), the Medieval Climate Anomaly (~1200–800 cal yr BP), and the Current Warm Period, which began around 100 cal yr BP. This record highlights the complexities of the LHDP, an interval that was more variable at June Lake than has been previously described in regional records.