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Lake Baikal is the largest freshwater lake in the world, accounting for about 20% of the world’s fresh surface water. The lake’s outflow to the ocean occurs only via the Angara River, which has several hydroelectric power plants (HPPs) along its watercourse. The first such HPP, Irkutsk HPP, was built in 1956 and is located 60 km from the Angara River’s source. After two years, the backwater from this HPP expanded to the lake shores and began raising the Baikal Lake level. Currently, there is a dynamic balance between the new lake level, the lake inflow from its tributaries, and the Angara River discharge through the Irkutsk HPP. However, both the Angara River discharge and the Baikal Lake level were distorted by the HPP construction. Thus, to correct understanding the changes in the lake level for the past century due to climatic changes, we first needed to estimate naturalized lake levels that would be if no HPP was ever built. This was an important task that allowed (a) the actual impact of global changes on the regional hydrological processes to be estimated and (b) better management of the HPP itself to be provided through future changes. With these objectives in mind, we accumulated multi-year data on the observed levels of Lake Baikal, and components of its water budget (discharge of main tributaries and the Angara River, precipitation, and evaporation). Thereafter, we assessed the temporal patterns and degree of coupling of multi-year and intra-annual changes in the lake’s monthly, seasonal, and annual characteristics. The reconstruction of the average monthly levels of Lake Baikal and the Angara River water discharge after the construction of the Irkutsk HPP was based on the relationship of the fluctuations with the components of the Lake water budget before regulation. As a result, 123-year time series of “conditionally natural” levels of Lake Baikal and the Angara River discharge were reconstructed and statistically analyzed. Our results indicated high inertia in the fluctuations in the lake level. Additionally, we found a century-long tendency of increases in the lake level of about 15 cm per 100 years, and we quantified the low-frequency changes in Lake Baikal’s water levels, the discharge of the Angara River, and the main lake tributaries.