Large-scale climate change is superimposed on interacting patterns of climate variability that fluctuate on numerous temporal and spatial scales--elements of which, such as seasonal timing, may have important impacts on local and regional ecosystem forcing. Lake Baikal in Siberia is not only the world's largest and most biologically diverse lake, but it has exceptionally strong seasonal structure in ecosystem dynamics that may be dramatically affected by fluctuations in seasonal timing. We applied time-frequency analysis to a near-continuous, 58-year record of water temperature from Lake Baikal to examine how seasonality in the lake has fluctuated over the past half century and to infer underlying mechanisms. On decadal scales, the timing of seasonal onset strongly corresponds with deviation in the zonal wind intensity as described by length of day (LOD); on shorter scales, these temperature patterns shift in concert with the El Nino-Southern Oscillation (ENSO). Importantly, the connection between ENSO and Lake Baikal is gated by the cool and warm periods of the Pacific Decadal Oscillation (PDO). Large-scale climatic phenomena affecting Siberia are apparent in Lake Baikal surface water temperature data, dynamics resulting from jet stream and storm track variability in central Asia and across the Northern Hemisphere.