Recent human population growth has contributed to the degradation of environmental resources in Guatemala. Since 1900, the population of the country grew from < 1 to > 17 million inhabitants. The watershed of Lake Izabal, eastern Guatemala, also experienced rapid population growth, and with it, development of intensive agriculture in areas adjacent to the lake. These recent demographic and land-use changes altered anthropogenic nutrient inputs to the water body, through delivery of raw sewage, and agricultural practices that include excessive use of fertilizers. Currently, Lake Izabal is marked by frequent algal blooms and associated fish-kill events. It also hosts a number of invasive, and in some cases, exotic plant and animal species. We used data from a sediment core collected in the western end of the lake to link past anthropogenic activities in the watershed to the deterioration of water quality and shifts in aquatic ecosystem functioning. We measured total organic carbon (TOC), total nitrogen (TN), and δ13C and δ15N of organic matter in a 137Cs- and 14C-dated sediment core from the Polochic Delta in Lake Izabal to infer past limnological changes. The core chronology indicates that 505 cm of sediment accumulated in only the last 370 years (~ 1.4 cm a−1). TOC and TN concentrations increased since about 1950, a time during which the TOC:TN ratio decreased, indicating a relatively greater contribution of phytoplankton to the sediment organic matter. Stratigraphic shifts in δ13C and δ15N indicate recent increasing inputs of raw sewage and fertilizer to the lake during the same time period. Lake Izabal, like many other water bodies in Guatemala, is starting to undergo cultural eutrophication, which probably accounts for the frequent algal blooms, proliferation of invasive species (e.g. Hydrilla verticillata), and decline in fish abundance.