Surface sediments (n=41) reflecting modern times (uppermost 10 cm) were collected during a November/December 2018 field campaign along the course of the Mkhuze River and a transect into Lake St. Lucia (KwaZulu Natal Province, South Africa). In addition, plant species (n=10) were collected based on previous reports of dominant vegetation communities and local occurrences. All samples were extracted soon after with a mixture of dichloromethane and methanol (9:1), purified, and fractionated. The apolar fraction was finally analyzed for its n-alkane concentrations and corresponding compound-specific carbon and hydrogen isotope compositions. Sub-samples of the surface sediments were also analyzed for (i) organic matter content (total organic carbon) and composition (d13C, carbon-to-nitrogen ratio) after decalcification, and (ii) for thermal indices (Hydrogen Index, R-index, I-index) using Rock-Eval analyses. The study's objective was to evaluate the most extensive freshwater wetland system in South Africa regarding its current condition and functioning by identifying the origin and transport pathways of sedimentary organic matter.