Recent warming in the Andes is affecting the region’s water resources including glaciers and lakes, which supply water to tens of millions of people downstream. High-elevation wetlands, known locally as “bofedales”, are an understudied Andean ecosystem despite their key role in carbon sequestration, maintenance of biodiversity, and regulation of water flow. Here, we analyze subfossil diatom assemblages and other siliceous bioindicators preserved in a peat core collected from a bofedal in Peru’s Cordillera Vilcanota. Basal radiocarbon ages show the bofedal likely formed during a wet period of the Little Ice Age (1520–1680 CE), as inferred from nearby ice core data. The subfossil diatom record is marked by several dynamic assemblage shifts documenting a hydrosere succession from an open-water system to mature peatland. The diatoms appear to be responding largely to changes in hydrology that occur within the natural development of the bofedal, but also to pH and possibly nutrient enrichment from grazing animals. The rapid peat accretion recorded post-1950 at this site is consistent with recent peat growth rates elsewhere in the Andes. Given the many threats to Peruvian bofedales including climate change, overgrazing, peat extraction, and mining, these baseline data will be critical to assessing future change in these important ecosystems.