The study of abrupt changes in global climate requires high-resolution records for which the connection to the climate system is well understood. Because lake systems are by their nature unique, ground truthing of geochemical measurements against directly observable physical evidence is required. The Mono Lake basin exposes multiple outcrops of lake sediments deposited during the last glacial period, providing the opportunity to reconstruct lake-level changes through stratigraphy-based interpretation of high-resolution records. Here we present a record of bulk-sediment carbonate derived from overlapping sections in three outcrops around the Mono Lake basin. We interpret this record as a reflection of lake-level variation, based on well-exposed stratigraphy and sedimentary facies changes. The co-variation of lake level with Sr isotopes measured in ostracodes is interpreted to reflect increased proportion of water supplied from the eastern basin during wet times. This high carbonate–high lake-level relationship is the opposite of the high carbonate–low lake-level relationship inferred in nearby Owens Lake, a difference attributable to extreme differences in basin geometry affecting the frequency of spilling conditions and resultant lake chemistry.