The carbon isotope composition (d13C values) of long chain n-alkanes in lake sediments has been considered a reliable means of tracking changes in the terrigenous contribution of plants with C3 and C4 photosynthetic pathways. A key premise is that long chain leaf wax components used for isotope analysis are derived primarily from terrigenous higher plants. The role of aquatic plants in affecting d13C values of long chain n-alkanes in lacustrine sediments may, however, have long been underestimated. In this study, we found that a large portion of long chain n-alkanes (C27 and C29) in nearshore sediments of the Lake Qinghai catchment was contributed by submerged aquatic plants, which displayed a relatively positive carbon isotope composition (e.g. 26.7‰ to 15.7‰ for C29) similar to that of terrestrial C4 plants. Thus, the use of d13C values of sedimentary C27 and C29 n-alkanes for tracing terrigenous vegetation composition may create a bias toward significant overestimation/underestimation of the proportion of terrestrial C4 plants. For sedimentary C31, however, the contribution from submerged plants was minor, so that the d13C values for C31 n-alkane in surface sediments were in accord with those of the modern terrestrial vegetation in the Lake Qinghai region. Moreover, we found that changes in the d13C values of sedimentary C27 and C29 n-alkanes were closely related to water depth variation. Downcore analysis further demonstrated the significant influence of endogenous lipids in lake sediments for the interpretation of terrestrial C4 vegetation and associated environment/climate reconstruction. In conclusion, our results suggest that the d13C values of sedimentary long chain n-alkanes (C27, C29 and C31) may carry different environmental signals. While the d13C values of C31 were a reliable proxy for C4/C3 terrestrial vegetation composition, the d13C values of C27 and C29 n-alkanes may have recorded lake ecological conditions and sources of organic carbon, which might be affected by lake water depth.