We studied a 2200-year-old sediment core from Lake Zapovednoye, a small, deep, freshwater lake near the site of the 1908 Tunguska impact event. Analysis of the sediment core for geochemistry, pollen, chironomids, Cladocera, and diatoms revealed traces of climatic fluctuations during the investigated time period during which a cool climate before 1000 CE was replaced by the Medieval Climatic Optimum, the Little Ice Age, and finally the modern warming. An increased content of terrigenous elements was identified at the depth corresponding to ca. 1908 CE. This layer presumably resulted from erosion of the soil cover after the tree fall caused by the Tunguska impact event (the largest recorded in history). For the first time, the reaction of lake biota to an impact event has been detected. Our study has demonstrated that the taxonomic diversity of hydrobionts (chironomids and cladocerans) significantly declined after the catastrophe, probably due to increased turbidity, and recovered in 6–10 years. The pollen and diatom assemblages, however, demonstrated weaker compositional shifts.