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Abstract The¹⁴C content of sedimentary organic matter (OM) and specific organic molecules provide valuable information on the source and age of OM stored in sediments, but these data are limited for tropical fluvial and lake sediments. We analyzed¹⁴C in bulk OM, palmitic acid (C₁₆), and long‐chainn‐alkanoic acids (C₂₄, C₂₆, and C₂₈), within fluvial and lake sediments in the catchment of Lake Izabal, a large tectonic lake basin in Guatemala. We combined these measurements with bulk and compound‐specific δ¹³C measurements, as well as sediment organic carbon to nitrogen (OC:N) ratios, to understand the source and age of sedimentary OM in different regions of the lake catchment. Most fatty acid and bulk OM samples were characterized by pre‐modern carbon, indicating important input of aged carbon with residence times of hundreds to thousands of years into sediments. We identified two mechanisms leading to aged carbon export to sediments. In the high‐relief and deforested Polochic catchment, older OM and fatty acids are associated with low % total organic carbon (TOC) and low OC:N, indicating aged OM associated with eroded mineral soil. In the smaller, low‐relief, and largely forested Oscuro catchment, old OM and fatty acids are associated with high %TOC and high OC:N ratios, indicating export of undegraded aged plant biomass from swamp peat. The age of bulk OM and fatty acids in Lake Izabal sediments is similar to the ages observed in fluvial sediments, implying that fluvial input of aged soil carbon makes an important contribution to lake sediment carbon reservoirs in this large tropical lake.