Increasing surface air temperatures and human influences (e.g., agriculture, grazing, mining, urbanization, tourism) are altering lakes on the Andean páramo of South America, as illustrated by changes in diatom species composition in sediment cores from the region that span the last ~150 years. Previous studies were limited by their relatively short temporal scales and limited spatial coverage. We analyzed sediment cores from the northern (Laguna Piñan) and southern (Laguna Fondococha) Andean páramos of Ecuador. The deposits span the last two millennia and provide a longer-term perspective on past changes in lake ecological and geochemical dynamics.Both lakes show shifts in dominant diatoms through time. Dominant diatom taxa in Fondococha shifted between two Aulacoseira species, and there was a change in the planktic to benthic ratio, a proxy for open-water versus shallow-water habitats. Both changes are interpreted as evidence of fluctuating lake level. The inferred lake-level changes are corroborated by stratigraphic variations in the concentration of Ti, an erosional proxy, indicating changes in clastic input as a function of wetter or drier conditions. Piñan shows a directional shift in the diatom assemblage over the period of the record, from benthic diatoms tolerant of high dissolved organic carbon (DOC), low pH, and low nutrients, to an assemblage characteristic of lower DOC, higher pH, higher nutrients, and higher lake levels. Shifts in Piñan's diatoms are correlated with tephra layers in the sediment, suggesting that local volcanic ash deposition may have altered both the catchment and lake geochemistry. This is supported by relatively higher δ 13 C values in organic matter associated with tephra layers, which become more negative up-section. Our data suggest that remote lakes in spatially heterogenous montane regions are sentinels of environmental change, and the records from Piñan and Fondococha provide insights into Andean ecosystem responses to past environmental perturbations.