In recent decades, climate change in Peru’s Cordillera Vilcanota has resulted in massive reductions to its cryosphere and the upslope migration of species and agriculture. Little, however, is known about the response of the region’s many lakes that support local biodiversity and supply water to downstream populations. We analyzed fossil diatom assemblages in dated sediment cores from three lakes with differing morphometry and catchment characteristics to document the limnological response to climate variability over the late Holocene. The study lakes contained similar dominant diatom taxa but recorded markedly different assemblage shifts over time. The two deeper lakes, Laguna Sibinacocha (zmax = 92 m) and Chaca Cocha (zmax = 18 m), contained diatom assemblages that oscillated in dominance between benthic fragilarioids (Staurosirella pinnata, Pseudostaurosira brevistriata) and the planktonic Discostella stelligera. The Chaca Cocha diatom record closely matched the mean state changes in climate inferred from independent proxy records, whereas the record from the glacially influenced Laguna Sibinacocha did not match independent records. In contrast, the shallow study site, Lado del Quelccaya (zmax = 5 m), recorded a complacent diatom profile dominated by benthic fragilarioids with negligible planktonic taxa. The disparate diatom trajectories among the study lakes reflect variations in morphometry and glacial influence and the assemblage shifts appear best explained by climate-driven alterations to thermal stratification. These data offer insight into the primary mechanisms driving limnological change in this region and how different lake types throughout the Andes may respond to future warming.