While deposition of reactive nitrogen (N) in the twentieth century has been strongly linked to changes in diatom assemblages in high-elevation lakes, pronounced and contemporaneous changes in other algal groups suggest additional drivers. We explored the origin and magnitude of changes in two mountain lakes from the end of the Little Ice Age at ca 1850, to ca 2010, using lake sediments. We found dramatic changes in algal community abundance and composition. While diatoms remain the most abundant photosynthetic organisms, concentrations of diatom pigments decreased while pigments representing chlorophytes increased 200–300% since ca 1950 and total algal biomass more than doubled. Some algal changes began ca 1900 but shifts in most sedimentary proxies accelerated ca 1950 commensurate with many human-caused changes to the Earth System. In addition to N deposition, aeolian dust deposition may have contributed phosphorus. Strong increases in summer air and surface water temperatures since 1983 have direct and indirect consequences for high-elevation ecosystems. Such warming could have directly enhanced nutrient use and primary production. Indirect consequences of warming include enhanced leaching of nutrients from geologic and cryosphere sources, particularly as glaciers ablate. While we infer causal mechanisms, changes in primary producer communities appear to be without historical precedent and are commensurate with the post-1950 acceleration of global change.