Diatoms, combined with a multiproxy study of lake sediments (organic matter, N, δ15N, δ13C, biogenic silica, grain size, Cladocera and chironomids, Alnus pollen) from Lone Spruce Pond, Alaska detail the late-glacial to Holocene history of the lake and its response to regional climate and landscape change over the last 14.5 cal ka BP. We show that the immigration of alder (Alnus viridis) in the early Holocene marks the rise of available reactive nitrogen (Nr) in the lake as well as the establishment of a primarily planktonic diatom community. The later establishment of diatom Discostella stelligera is coupled to a rise of sedimentary δ15N, indicating diminished competition for this nutrient. This terrestrial-aquatic linkage demonstrates how profoundly vegetation may affect soil geochemistry, lake development, and lake ecology over millennial timescales. Furthermore, the response of the diatom community to strengthened stratification and N levels in the past confirms the sensitivity of planktonic diatom communities to changing thermal and nutrient regimes. These past ecosystem dynamics serve as an analogue for the nature of threshold-type ecological responses to current climate change and atmospheric nitrogen (Nr) deposition, but also for the larger changes we should anticipate under future climate, pollution, and vegetation succession scenarios in high-latitude and high-elevation regions.