Lignin phenol, pollen, and diatom analyses were performed on dated sediments (13,533–8993 cal yr B.P.) recovered from Fallen Leaf Lake, California. This multiproxy data set constrains the end of the Tioga glaciation in the Lake Tahoe Basin and reconstructs the response of the region’s aquatic and terrestrial ecosystems to climatic changes that accompanied the Younger Dryas, the end of the Pleistocene, and early Holocene warming. From the Pleistocene to the Holocene, lignin concentrations and syringyl/vanillyl (S/V) ratios increased, while cinnamyl/vanillyl (C/V) ratios and the lignin phenol vegetation index (LPVI) decreased, recording the proliferation of woody plant material and, particularly, the expansion of angiosperms as the Tioga glaciation ended and temperatures warmed. This interpretation is constrained by lignin phenol analyses of plant material from Fallen Leaf Lake’s present-day watershed. Complementary palynological analyses show a transition from a gymnosperm-dominated landscape to a more mixed angiosperm-gymnosperm vegetation assemblage that formed as closed canopy forests became more open and grasses and aster colonized meadows. Aquatic flora assemblages, in the form of greater amounts of green algae and greater percentages of diatom phytoplankton, indicate increased levels of lake primary productivity in response to warming. Principal component analysis (PCA) distinctly resolves the Pleistocene from the Holocene diatom flora. The Pleistocene flora is dominated by cyclotelloids and low-mantled Aulacoseira species that are rare in Fallen Leaf Lake today, but common at higher and colder elevations that may resemble the Pleistocene Fallen Leaf Lake. The Holocene diatom flora is dominated by Aulacoseira subarctica.