The effects of the Holocene climatic amelioration, productivity, and preservation on biogenic silica accumulation in the northern basin of Lake Baikal are evaluated by analyzing biogenic silica, organic carbon, nitrogen, and the stable carbon isotopic composition of organic matter in a 4 m piston core and a companion box core. In the early Holocene (11,000-8500 yr B.P.), biogenic silica accumulation was low because of low productivity, strong oligotrophy, and the influx of nutrient-limited alpine glacial meltwater. In the middle Holocene, productivity increased significantly during 8500-7000 yr B.P., but little biogenic silica accumulated in sediments because the dominant primary producer was not diatom flora and because of the relatively higher productivity caused by enhanced terrestrial nutrient influx. The highest accumulation rates of biogenic silica were those between 7000 and 4500 yr B.P., when aquatic productivity increased, limnological stratification occurred, a mature diatom flora developed. In the late Holocene (the past 4500 yr), biogenic silica accumulation decreased because of enhanced recycling and regeneration of silica and a low sedimentation rate.