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Southwestern North America is currently experiencing a multidecadal megadrought, with severe consequences for water resources. However, significant uncertainty remains about 21st century precipitation changes in this semi-arid region. Paleoclimatic records are essential for both contextualizing current change, and for helping constrain the sensitivity of regional hydroclimate to large-scale global climate. In this paper, we present a new 2.8 Ma to present compound-specific isotopic record from Clayton Valley, the site of a long-lived paleolake in the southern Great Basin. Hydrogen and carbon isotopes from terrestrial plant leaf waxes provide evidence of past shifts in rainfall seasonality as well as ecosystem structure, and help contextualize the formation of this lithium-rich lacustrine basin. Our results suggest that regional hydroclimates underwent a substantial reorganization at the Plio-Pleistocene boundary, especially between 2.6 and 2.0 Ma. In this interval, a reduced latitudinal temperature gradient in the North Pacific likely resulted in a northward shift in storm tracks, and a reduction in winter rainfall over the southern Great Basin. This occurred against a background of increased summer rainfall and a greater accumulation of lithium in the lake basin. Our interpretation is corroborated by a compilation of Plio-Pleistocene north Pacific sea surface temperature records, as well as an isotope-enabled model simulation. Overall, these results suggest that past shifts in rainfall seasonality helped set the stage for the development and dessication of lithium-rich lacustrine deposits.