Sediments in Lake Izabal, Guatemala, contain substantial lead (Pb), zinc (Zn), and nickel (Ni). The lack of historical data for heavy metal concentrations in the sediments makes it difficult to determine the sources or evaluate whether inputs of metals to the lake have changed through time. We measured the relative abundances and concentrations of Pb, Zn, and Ni by X-Ray Fluorescence core scanning and by Inductively Coupled Plasma Optical Emission Spectrometry in three sediment cores to explore stratigraphic distributions of metals in the lake deposits. High amounts of Pb and Zn in the core taken near the Polochic Delta suggest that galena and sphalerite mining increased Pb and Zn delivery to Lake Izabal between ~1945 and 1965 CE. An up-core Ni increase in the core taken near a different mine on the north shore of Lake Izabal suggests that recent nickel mining operations led to an increase in Ni concentrations in the local sediments, but amounts in the other cores indicate that Ni is not widely distributed throughout the lake. Sediment cores from Lake Izabal are reliable recorders of heavy metal input to the lake, and were measured to establish background metal levels, which would otherwise be unavailable. Concentrations of Pb, Zn, and Ni in older, pre-20th-century Lake Izabal sediments reflect input from natural erosion of bedrock. Our results provide previously unavailable estimates of background metal concentrations in Lake Izabal before the onset of mining. These results are necessary for future monitoring related to mining contamination of the lake ecosystem.