Abstract The Lake Baikal, containing one‐fifth of Earth’s unfrozen surface freshwater, faces increasing hydrological uncertainty under climate change. Its water balance depends on Selenga River inflow and Angara River outflow. We present a 343‐year combined Selenga and Angara streamflow reconstruction using a tree‐ring network to provide a multi‐century hydroclimatic baseline. The reconstruction captures intermittent drying trends throughout the 20th century, including a ∼90% streamflow decline from high levels, consistent with long‐term regional aridification. This trend has reversed sharply over the last decade showing a most sustained ∼80% increase. The recent hydrological recovery is consistent with basin‐wide vegetation greening, rising lake levels, and favorable eco‐climatic conditions, primarily improved water availability. Rapidly changing atmospheric circulations associated with a regional slowing Arctic‐amplified warming drive enhanced moisture transports. The contrasting trend between recent recovery and preceding long‐term decline underscores the need for adaptive management strategies to account for non‐stationary dynamics in safeguarding critical freshwater resources.