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Laguna Santa Elena (8.9290° N, 82.9257° W, 1055 m a.s.l.) is a small lake in the Diquís archaeological sub-region of southern Pacific Costa Rica. Previous analyses of pollen and charcoal in a sediment core from Santa Elena revealed a nearly 2,000 year history of vegetation change, maize cultivation and site occupation that is consistent with the archaeological record from the lake basin and surrounding area. Here we present the results of new loss-on-ignition, geochemical and bulk stable carbon (δ13C) and nitrogen (δ15N) isotope analyses of the Santa Elena sediments that supplement and refine the previous reconstruction. Like many lakes in Central America and the Caribbean, Laguna Santa Elena was a magnet for humans throughout its history. As a result, the lake experienced vegetation modification by humans and maize cultivation at varying intensities over a long duration. The Santa Elena sediments provide a record of palaeoenvironmental change during times of major culture change and increasing cultural complexity in the Diquís region, which occurred during intervals of broader changes driven by external forcing mechanisms, including the Terminal Classic Drought (TCD), the Little Ice Age (LIA) and the Spanish Conquest. Our high resolution lake sediment study from Santa Elena reveals details of these events at the local scale that are unobtainable by other means, including the timing of the initial intensification of maize cultivation at ca. 1,570 cal BP (AD 380) and two intervals of population decline coinciding with the TCD at ca. 1,085 cal BP (AD 865) and near the start of the LIA at ca. 683 cal BP (AD 1267).