Understanding past climate and environmental conditions depends largely on accurate interpretations of proxy records from a range of environments, including tropical wetlands and lakes. Lipid biomarker analysis can provide important information about the sources of the accumulated organic material, and thus about the environmental information contained therein. Here we use n -alkane distributions and stable carbon isotopes of leaf waxes (δ 13 C wax ) to identify the sources of organic matter (OM) of a 2000-year long sediment/peat record from Lake Pa Kho (LPK) in northeastern Thailand, and to constrain the mechanisms that cause shifts in δ 13 C wax and in δ 13 C of bulk organic matter (δ 13 C bulk ). Our results show three main sources of OM: terrestrial plants, aquatic macrophytes and algae. The δ 13 C values of the long chain n -alkanes, show two distinct groups: C 27 –C 31 and C 33 –C 35 n -alkanes, where the δ 13 C values of C 33 –C 35 n -alkanes reflect that of δ 13 C bulk . Lower moisture availability on the wetland, known from other sedimentary evidence, was characterized by low carbon isotope values typically seen for C3 plants, whereas greater moisture availability corresponded to higher δ 13 C values (around −20‰) of C 33 –C 35 n -alkanes, resembling a typical C4 plant signal. However, various lines of evidence argue against large shifts between C3 and C4 plant input. Instead, we suggest that the high δ 13 C values were indirectly caused by higher aquatic productivity during periods of greater moisture availability, decreasing dissolved CO 2 , but increasing bicarbonate availability caused by higher pH. This caused the dominant macrophytes (e.g., Potamogeton spp.) to shift their carbon source from CO 2 to bicarbonate, which has much higher δ 13 C values. Our results show that the environmental context should be taken into account when interpreting n -alkane δ 13 C variability as a paleo-environmental/climatic signal as this contains several important variables that need to be disentangled and explained.