N-alkane-based proxies are widely employed to reconstruct paleoclimate and paleoenvironment in lacustrine environments. However, little is known about the influence of microbially mediated alkane-degradation on n-alkane-derived proxies. In this study, the chemical composition of n-alkanes and microbially mediated n-alkane degradation potential were investigated in the surface sediment samples collected from seven lakes with a range of salinity from freshwater to salt saturation on the northern Qinghai-Tibetan Plateau (QTP). The results showed that the chemical composition of n-alkanes differed among the studied QTP lakes. Significant correlations were observed between salinity and some n-alkane-based paleoclimate and paleoenvironment proxies, such as ratio of C21−/C22+, average chain length (ACL) and carbon preference index (CPI). This suggested that salinity may affect the validity of some n-alkane-based paleoclimate and paleoenvironment proxies. Alkane-degrading bacteria were abundant and widespread in the studied freshwater and saline/hypersaline lakes but were minor or absent in salt-saturation lakes. The obtained alkane-degrading bacterial strains showed active ability to degrade n-hexadecane. This suggested that the salinity influence on the n-alkane distribution may be partially related to microbial degradation, which awaits further in-situ investigation. So salinity variation should be taken into account when using n-alkane-based proxies for reconstructing paleoclimate and paleoenvironment in lakes. •Chemical composition of n-alkanes differed among the studied lakes of different salinity•Salinity may affect the validity of n-alkane-based paleoclimate proxies.•Alkane-degrading bacteria showed active ability to degrade n-hexadecane.•Microbial degradation may partially account for salinity influence on n-alkane distribution.•Salinity variation should be taken into account when using n-alkane-based proxies.