Northern high‐latitude lakes are undergoing climate‐induced changes including shifts in their hydrologic connectivity with terrestrial ecosystems. How this will impact dissolved organic matter (DOM) biogeochemistry remains uncertain. We examined the drivers of DOM composition for lakes in the Yukon Flats Basin in Alaska, an arid region of low relief that is characteristic of over one‐quarter of circumpolar lake area. Utilizing the vascular plant biomarker lignin, chromophoric dissolved organic matter (CDOM), and ultrahigh‐resolution mass spectrometry, we interpreted DOM compositional changes using lake‐water stable isotope (δ¹⁸O‐H₂O) composition as a proxy for lake hydrologic connectivity with the landscape. We observed a relative decrease in CDOM in more hydrologically isolated lakes (enriched δ¹⁸O‐H₂O) without a corresponding decrease in dissolved organic carbon (DOC) concentration. Although DOC and CDOM were weakly correlated, a significant positive relationship between lignin and CDOM (r² = 0.67) demonstrates that optical parameters are useful for estimating lignin concentration and thus vascular plant contribution to lake DOM. Indicators of allochthonous DOM, including lignin carbon normalized yields, CDOM aromaticity proxies, and relative abundances of polyphenolic and condensed aromatic compound classes, were negatively correlated with δ¹⁸O‐H₂O (r² > 0.45), suggesting there is little allochthonous DOM supplied to many of these hydrologically isolated lakes. We conclude that decreased lake hydrologic connectivity, driven by ongoing climate change (i.e., decreased precipitation, warming temperatures), will reduce allochthonous DOM contributions and shift lakes toward lower CDOM systems with ecosystem‐scale ramifications for heat transfer, photochemical reactions, productivity, and ultimately their biogeochemical function.