The Cochabamba Basin (Bolivia) is on the ancient road network connecting Andean and lowland areas. Little is known about the longevity of this trade route or how people responded to past environmental changes. The eastern end of the Cochabamba valley system constricts at the Vacas Lake District, constraining the road network and providing an ideal location in which to examine past human–environmental interactions. Multiproxy analysis of sediment from Lake Challacaba has allowed a c. 4000 year environmental history to be reconstructed. Fluctuations in drought tolerant pollen taxa and calcium carbonate indicate two periods of reduced moisture availability (c. 4000–3370 and c. 2190–1020 cal yr BP) compared to adjacent wetter episodes (c. 3370–2190 and c. 1020 cal yr BP–present). The moisture fluctuations broadly correlate to El Niño/Southern Oscillation variations reported elsewhere. High charcoal abundance from c. 4000 to 2000 yr ago indicates continuous use of the ancient road network. A decline in charcoal and an increase in dung fungus (Sporormiella) c. 1340–1210 cal yr BP, suggests that cultural changes were a major factor in shaping the modern landscape. Despite undisputable impacts of human populations on the Polylepis woodlands today, we see no evidence of woodland clearance in the Challacaba record.