The Arctic is the fastest-warming region on Earth, causing vegetation to expand into areas previously dominated by snow and ice, exacerbating warming further. The need for accurate paleoclimate reconstructions in the Arctic is thus crucial, and aquatic and terrestrial plant leaf wax hydrogen isotope values are valuable proxies for past climate. However, it can be difficult to distinguish aquatic from terrestrial waxes in lake sediments, which can lead to uncertainty surrounding interpretations of past climate. We quantify the leaf wax n-alkanoic acid chain length distributions (C20, C22, C24, …, C32) of n = 8 modern lake sediments and n = 30 species of modern plants from Lake Qaupat (QPT) on southern Baffin Island to track leaf wax production and deposition in a modern Arctic lake setting. We assess variability among modern plant chain length distributions using principal component analysis (PCA), and passively plot the sediments along these axes. We find that submerged aquatic plants, including four mosses and one graminoid, and lake sediments plot closely on the PCA biplot, indicating submerged aquatic plants contribute large portions of waxes to modern lake sediments. We adapt the Stable Isotope Mixing Models in R (simmr) package to use relative plant wax distributions as variables, and input distributions for the most abundant modern and Holocene plants, determined using vegetation mapping and sedimentary ancient DNA, respectively. We apply the model to QPT’s downcore leaf wax distribution record to estimate plant contributions to lake sediment waxes during the mid- to late-Holocene. Model results indicate that Arctic shrub Salix arctica is the primary wax source (0.73 ± 0.06) to lake sediments until ~1.3 ka, after which submerged moss becomes the primary wax source (0.57 ± 0.23) to lake sediments until present. However, d2H analysis on modern Salix spp. (n = 3 S. arctica and 1 S. reticulata), submerged aquatic plant samples (n = 3 Eleocharis acicularis), and lake surface sediments (n = 4) all indicate it is unlikely that Salix spp. is the primary wax source to sedimentary mid-chain waxes: the most depleted C22 d2H value measured on Salix spp. samples is -200‰, while the most enriched C22 d2H value measured on modern lake sediments is -240‰. Furthermore, lake sedimentary C22 d2H does not exceed -230‰ throughout the entire QPT leaf wax record. E. acicularis samples collected from the edges of the main QPT basin have C22 d2H values between -231 and -234‰, suggesting that submerged aquatic plants are a more likely source of mid-chain waxes in QPT lake sediments. For sedimentary long-chain waxes in QPT, on the other hand, it remains unclear if they are primarily sourced from terrestrial plants, or reflect an integrated aquatic and terrestrial signal, and future studies should focus on quantifying wax transport to lake sediments.