Abstract We present original data on fluxes of particulate matter through a 1366 m thick water column, measured with sediment traps near the Neutrino Telescope Station in South Baikal. The research was part of a long-term international research project which started in March 1999 in order to investigate current sedimentation in the lake. The total flux of sedimenting particles was considerably higher in 2000 as compared with 1999. This was due to the exceptional growth of siliceous diatoms of the genus Aulacoseira in 2000, leading to the so-called Melosira year. Biogenic silica is predominant in the particulate matter and might reach 56%, while the concentrations of organic carbon and total nitrogen do not exceed 16% and 1%, respectively.