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Micro-X-ray fluorescence scanning spectroscopy of marine and lake sedimentary sequences can provide detailed palaeoenvironmental records through element intensity proxy data. However, problems with the effects of interstitial pore water on the micro-X-ray fluorescence intensities have been pointed out. This is because the X-ray fluorescence intensities are measured directly at the surfaces of split wet sediment core samples. This study developed a new method for correcting X-ray fluorescence data to compensate for the effects of pore water using a scanning X-ray analytical microscope. This involved simultaneous use of micro-X-ray fluorescence scanning spectroscopy and an X-ray transmission detector. To evaluate the interstitial pore water content from the X-ray transmission intensities, a fine-grained sediment core retrieved from Lake Baikal (VER99-G12) was used to prepare resin-embedded samples with smooth surfaces and uniform thickness. Simple linear regression between the linear absorption coefficients of the samples and their porosity, based on the Lambert-Beer law, enabled calculation of the interstitial pore spaces and their resin content with high reproducibility. The X-ray fluorescence intensities of resin-embedded samples were reduced compared with those of dry sediment samples because of: (i) the X-ray fluorescence absorption of resin within sediment; and (ii) the sediment dilution effects by resin. An improved micro-X-ray fluorescence correction equation based on X-ray fluorescence emission theory considers the instrument's sensitivity to each element, which provides a reasonable explanation of these two effects. The resin-corrected X-ray fluorescence intensity was then successfully converted to elemental concentrations using simple linear regression between the data from micro-X-ray fluorescence scanning spectroscopy and from the conventional analyzer. In particular, the calculated concentration of SiO2 over the depth of the core, reflecting diatom/biogenic silica concentration, was significantly changed by the calibrations, from a progressively decreasing trend to an increasing trend towards the top of the core.