Lagoa do Caçò is an equatorial lake in northeast Brazil, where the Inter-Tropical Convergence Zone (ITCZ) enters the South American continent, and so at a key position for deciphering Quaternary climatic variation. Preliminary results have shown that the sedimentary organic matter (OM) in the lake records the shifts in the ITCZ since the Last Glacial Maximum. The nature and fate of the OM have been determined by studying surface sediments and potential OM sources. We present here the results of organic petrographic and Rock-Eval pyrolysis analytical assessments of the biological origin and preservation state of the OM in modern sediments from two deep transects of the lake. The results led us to understand how an oligotrophic lake has accumulated 6 m of OM-rich sediment during the last 20 kyr. Palaeoenvironmental studies have shown that the lake level fluctuated during this time. Our results explain the influence of lake bathymetric variation on early diagenesis and enable interpretation of the corresponding sedimentary OM record, which is dependent on the bathymetric variation.