Pre-Hispanic artifacts and sacred architecture were recently discovered submerged in a large lake (Laguna Sibinacocha) in the Peruvian Andes. The underwater ruins indicate a dramatic shift in the region’s hydrology but the timing and triggers of this shift remain unknown. In a novel approach blending archaeology and paleoecology, we analyzed a sediment sequence from within one of the recovered artifacts, specifically a pot from the Late Intermediate Period (~1000–1400 CE). Radioisotopic dating of discrete sediment intervals sampled from the pot show a stratigraphically intact profile that preserves a history of change at this site. The pot’s basal sediment age places the timing of lake-level rise at ~1600 CE, which post-dates the end of the Inca Empire (1400–1532 CE) by several decades. The ubiquity of planktonic algae throughout the sediment profile suggests water levels remained high above the pot since its submergence. Paleoclimate data from the nearby Quelccaya ice core records indicate lake flooding followed a pronounced wet period beginning ~1520 CE. These data show the permanence of mean state changes in climate on the region’s hydrology, with clear implications for the study site (an important water resource for ~500,000 people) and other lakes in the rapidly warming Andes.