The relative proportion of mid-chain to long chain n-alkane homologues and isotopic compositions of total organic carbon (Paq and δ13Corg) have been proposed as potential lake-level proxies since such features mainly come from submerged aquatic plants living within an optimum range of lake water depth. With limited dataset available, the applicability of both indices and their sensitivity to lake water depth changes across a broad geographic extent need further investigation. Here we report Paq and δ13Corg values in surface sediments collected from 55 lakes in mid-latitude Asia. We have found an arched relationship between Paq index and water depth, with high Paq values occurring at the depth of ~1–10 m, while sediments from shallower and deeper water lakes have relatively low Paq values. δ13Corg variation resembles an arched pattern with depth in freshwater and brackish lakes, with relatively high δ13Corg values also corresponding to the depth of ~1–10 m, but substantially high δ13Corg values in hypersaline environments (salinity > ~100,000 mg/L) obscure the arched δ13Corg-depth relationship. We suggest that both indices respond to the structure of aquatic plant community, especially the biomass of submerged plants. Our results confirm that Paq and δ13Corg can be used to infer lake-level changes in mid-latitude Asia, but other influencing factors have to be considered before applying the two proxies to down-core reconstructions, and combined utilization of the Paq and δ13Corg indicators could improve the reliability of paleohydrological reconstructions.