Using a set of surface sediment samples and corresponding macrophytes from the Tibetan Plateau, we show that aquatic macrophytes strongly influence the carbon isotope values of organic matter (OM), both total organic carbon (TOC) and compound specific, in lake sediments, which is often neglected when these proxies are interpreted in palaeoenvironmental studies. Assessments on the basis of a binary isotopic model revealed an average contribution from submerged macrophytes of up to 60% (mean 40%) to TOC and up to 100% (mean 66%) to mid-chain n-alkanes (C23 and C25). Submerged aquatic macrophytes contained typical mid-chain dominated n-alkane patterns in most of the samples, but also synthesized higher relative amounts of long chain homologues in shallower lakes - possibly due to adaptation to partial exposure to air. Macrophytes showed wide ranges of δ13C values for bulk OM (-18.1 to -5.8‰) and n-alkanes (e.g. -25.2 to -13.3‰ for n-C25 in Potamogeton) because of bicarbonate metabolism in the alkaline lakes. There is a highly significant correlation between δ13C values of lipids and bulk biomass in plant samples, but the offset between the two parameters increases with increasing value for the bulk biomass. In most of the sediment samples, the OM was strongly influenced by aquatic macrophytes, with respect to both n-alkane patterns and δ13C values. Wide ranges of values for TOC were observed (-29.0 to -16.0‰) as well as for mid-chain n-alkanes (e.g. -34.1 to -16.6‰ for n-C25), while the variability in long chain n-alkanes (C27, C29, C31) was relatively small. Our results further indicate that, in regions where C4 vegetation is absent, the relative contribution of submerged macrophytes to sediments can, in addition to n-alkane patterns, be assessed quantitatively from sedimentary δ13C values. © 2010 Elsevier Ltd.