The modern distribution of biogenic silica (SiO2biog) in Baikal surface (0–0.2 and 0–0.5 cm) sediments, its mass accumulation rates (MAR), and the processes responsible for this distribution were studied. The contents of SiO2biog were determined in samples from 87 stations evenly distributed throughout the lake water area. These data were used to calculate the MAR of SiO2biog and compile SiO2biog and MAR distribution maps. The maps showed that the MAR varies significantly throughout the study area. Its highest values have been established in North Baikal. In Central and South Baikal the MAR values are much lower, and the minimum values are observed in the Selenga shoal. This MAR distribution pattern is consistent with the distribution of frustules of Aulacoseira baicalensis endemic diatoms throughout the surface sediments. Compared with other modern diatom species, this one has the most massive and heaviest frustules, which undergo the least dissolution when settling. This suggests that the above species plays a leading role in the accumulation of biogenic silica in modern Baikal bottom sediments, whereas the role of thin-walled species is minor because of their small mass and partial or complete dissolution in water on settling. Dilution of the sediments with terrigenous material is less significant for the SiO2biog accumulation.