Investigations of how past human societies managed during times of major climate change can inform our understanding of potential human responses to ongoing environmental change. In this study, we evaluate the impact of environmental variation on human communities over the last four millennia in the southern Lake Titicaca basin of the Andes, known as Lake Wiñaymarka. Refined paleoenvironmental reconstructions from new diatom-based reconstructions of lake level together with archaeological evidence of animal and plant resource use from sites on the Taraco Peninsula, Bolivia, reveal frequent climate and lake-level changes within major cultural phases. We posit that climate fluctuations alone do not explain major past social and political transformations but instead that a highly dynamic environment contributed to the development of flexible and diverse subsistence practices by the communities in the Titicaca Basin.