Trace and rare earth elements from a Lake Peten Itzá (Guatemala) sediment core depict the geochemical dynamics affecting the lake from ~5500 y BP to the present. This timing encompasses the Preclassic (4000 to 1700 y BP) and Classic Periods (1700-1000 y BP) when thriving Maya societies extensively cleared land for agriculture. We demonstrate that this land use occurred during times of increased precipitation, where both processes resulted in increased erosion. Rare earth element ratios depict high precipitation rates between 3000 to 1000 y BP, correlating with an increase in allocthonous silicate input and low organic carbon in the “Maya Clay” stratigraphic section, where this layer is ascribed to intensive anthropogenic land use. Cesium anomalies provide additional evidence for runoff due to high rainfalls and amplified by anthropogenic impacts. The Peten Itzá core contains anomalous spikes of arsenic and mercury, where these peaks correspond to documented volcanic eruptions, and therefore are likely due to natural causes. The geochemical composition of sediments and palynological records indicate a re-growth of the forest after ~900 y BP. This increased forest vegetation coincides with the timing of the decline in Maya agriculture.