Synchrotron-based X-ray absorption near edge structure (XANES) spectroscopy was applied to study sulfur species in the sediments of Lake Biwa. Samples were collected at Nagahama Port where muddy substances were deposited all year around. The XANES analysis revealed the presence of reduced inorganic S (e.g. FeS, FeS₂, and element S), reduced organic S (e.g. methionine), intermediate S (e.g. sulfonate), and oxidized S (e.g. sulfate). By storing the sediments under aerobic condition, the most reduced inorganic S nearly faded out after seven months, and oxidized S increased extremely. On the contrary, under anaerobic condition, the population of each species remained unchanged, except a slight decrease of the most reduced inorganic S in the first week, which might be due to biological oxidization. It is proved that XANES is not only a non-invasive method to determine the chemical states of S species in the sediments, but also to trace the oxidation state of the sediment consisting of solid and liquid.