We reconstruct ancient temperature and elevation gradients across the early Eocene (52–49 Ma) northern Sierra Nevada (California, United States) using organic molecular proxies that record atmospheric and ground-level effects of topography. Paleoelevation was determined by reconstructing the change in the hydrogen isotopic composition of precipitation (ΔδDprecip) and mean annual temperature (ΔTGDGT) (glycerol dialkyl glycerol tetraethers) from the isotopic composition of fossil angiosperm leaf n-alkanes and the distribution of microbially produced soil tetraethers preserved in leaf-bearing sediments. Organic molecular data produce equivalent range-scale (δDn-alkane) and channel (TGDGT) paleoelevation estimates that show the northern Sierra Nevada was a warm (>6–8 °C warmer than modern), high-elevation (>2 km), and moderate- to low-relief landscape at the Eocene Climatic Optimum. Modern northern Sierra Nevada topography likely reflects post-Paleocene reduction of mean surface elevation and late Cenozoic increases in relief.