n-Alkane biomarker distributions in sediments from Swamp Lake (SL), in the central Sierra Nevada of California (USA), provide evidence for an increase in mean lake level ~ 3000 yr ago, in conjunction with widespread climatic change inferred from marine and continental records in the eastern North Pacific region. Length distributions of n-alkane chains in modern plants growing at SL were determined and compared to sedimentary distributions in a core spanning the last 13 ka. As a group, submerged and floating aquatic plants contained high proportions of short chain lengths (< nC25) compared to emergent, riparian and upland terrestrial species, for which chain lengths > nC27 were dominant. Changes in the sedimentary n-alkane distribution over time were driven by variable inputs from plant sources in response to changing lake level, sedimentation and plant community composition. A shift toward shorter chain lengths (nC21,nC23) occurred between 3.1 and 2.9 ka and is best explained by an increase in the abundance of aquatic plants and the availability of shallow-water habitat in response to rising lake level. The late Holocene expansion of SL following a dry mid-Holocene is consistent with previous evidence for increased effective moisture and the onset of wetter conditions in the Sierra Nevada between 4.0 and 3.0 ka.