This dataset presents concentrations of long-chain n-alkanes (nC25–nC33) and derived molecular indices, including Carbon Preference Index (CPI), Average Chain Length (ACL), and Paq, from Holocene marine sediment cores MDBT 557 and MDBT 561, recovered from the southern Brazilian continental shelf. Lipid biomarkers were extracted using organic solvents, purified by column chromatography, and quantified by gas chromatography with flame ionization detection (GC-FID), with surrogate standards used to assess analytical recovery. These data characterize variations in terrigenous organic matter input, vegetation-related signals, and hydrological conditions affecting the continental margin during the Holocene.