We present results of study of the bottom sediments of proglacial Lake Ekhoi, which is fed with the Peretolchin Glacier meltwater (East Sayan). The bottom deposit sequence, formed from 1885 to 2013, was investigated with a year–season time resolution, using X-ray fluorescence with synchrotron radiation (with and without scanning), the Fourier-transform infrared (FTIR) analysis, and color processing of core photos. The depth–age model of the core was based on counting of annual laminate layers with control by 210Pb, 137Cs, 238U, and 226Ra chronology. Intense glacier thawing was calculated from the amount of clastic matter supplied by the glacier meltwater into the lake. The elemental composition of the bottom sediments includes three groups reflecting periods of displacement of the glacier front and the intensity of evolution of aquatic biota. The first group of elements (Ca, K, Ti, Fe, and Mn) characterizes the supply of clastic matter without serious changes in the glacier edges. The second group (Ni, Cu, Br, and U) is responsible for the intensity of evolution of aquatic biota. Finally, the third group (Rb, Sr, Zr, Nb, Y, and Th) can describe the intensity of displacement of the glacier front. Intensive glacier thawing has proceeded since 1920; however, the glacier retreat was insignificant till 1947. From 1947 to 1970, the glacier rapidly retreated, especially in the period 1953–1970. This was induced by steady high regional summer surface temperature in 1938–1970. The following glacier retreat was during 1980–2000, synchronously with the global temperature anomaly in the Northern Hemisphere. Since 2000, the melting has slowed.