New methods for creating quantitative reconstructions of water levels in salt lakes during the Late Holocena using data from high-resolution X-ray fluorescence microanalysis with beams of synchrotron radiation allow a unique reconstruction of Lake Shira’s water levels over the last 1500 years on an annual time scale. Varvochronology (the counting of varves in bottom sediments) is used to constructing a time model of sedimentation, enabling us to estimate the reservoir effect that introduces error into datings of the bottom sediments of Lake Shira with respect to the supply of “ancient” carbon into lake. The obtained results can be used in quantitative assessments of the patterns of aridization in southern Siberia during the Late Holocene.