Measurements of Fourier transform infrared spectroscopy (FTIRS) in the mid-infrared (MIR) region were conducted on sedimentary records from Lake El'gygytgyn, NE Siberia, and Lake Ohrid, Albania/Macedonia. Calibration models relating FTIR spectral information to biogeochemical property concentrations were established using partial least squares regression (PLSR). They showed good statistical performance for total organic carbon (TOC), total nitrogen (TN), and biogenic silica (opal) in the sediment record from Lake El'gygytgyn, and for TOC, total inorganic carbon (TIC), TN, and opal in sediments from Lake Ohrid. In both cases, the calibration models were successfully applied for down-core analysis. The results, in combination with the small amount of sample material needed, negligible sample pre-treatments, and low costs of analysis, demonstrate that FTIRS is a promising, cost-effective tool that allows high-resolution paleolimnological studies.