Freshwater ecosystems are a major feature of the northern landscapes that are expected to experience significant future changes due to climate change and land-use alterations. In Central Yakutia, abundant lakes in topographic permafrost-thaw depressions, named ‘alaas’, define the traditional cultural landscape that is home to the indigenous Sakha people, with critical ecosystem services like freshwater supply, meadows for cattle breeding, as well as fishing and hunting grounds. In contrast, lakes in the Verkhoyansk mountain region east of Central Yakutia are of glacial origin or developed on glacial moraines and represent deeper and more oligotrophic lake systems much less used as human resources.</p> <p>Here, we analyse the hydrochemistry, sedimentary DNA (sedDNA)-derived aquatic plant diversity, geomorphology, and adjacent land cover of sixty-six lakes across the Central Yakutian lowland permafrost landscape and the Verkhoyansk Oymyakon high mountain plateau to understand their characteristics and environmental drivers. Our hydrochemical analysis reveals a clear distinction between the low-mineralised mountain lakes and the highly variable hydrochemistry of the lowland thermokarst lakes. The lake developmental stage within the thermokarst lake sequence seems to be a key driver of lake hydrochemistry in the lakes of the Central Yakutian lowland. Specifically, the lake’s developmental stage is reflected by dissolved organic carbon (DOC), pH, its stable isotopic composition, and the hydrochemical facies of alkali and earth alkali elements. New thermokarst lakes have a depleted stable isotopic composition, possibly due to contributions from meltwater of adjacent permafrost ground-ice. This thermokarst lake stage is typically located within forest and has the highest DOC. In contrast, the hydrologically open thermokarst lake systems, typically located in large connected alaas systems with settlements and managed land use, have lower DOC and fewer mineralisation than recently formed thermokarst lakes or old alaas lakes. The dilution in the hydrologically connected alaas lakes occurs due to flushing, mainly during high discharge events such as the regular snowmelt. Old alaas lakes show an enriched oxygen isotope composition and have high salinity and mineral content, suggesting processes of evaporation and highlighting their vulnerability to future warming. However, low chloride together with an enriched isotopic composition and elevated fluoride characterise several of the sampled high-salinity lakes. This points to an additional process beyond the current evaporation, such as fluoride leakage from lacustrine sediments or salt deposits.</p> <p>SedDNA-derived macrophyte diversity reflects lake types and reveals the dominance of brackish water-tolerant cosmopolitan submerged macrophytes, particularly <em>Stuckenia</em> and <em>Potamogeton</em>, across all lake types. The macrophytes <em>Myriophyllum </em>and <em>M</em>. <em>verticillatum</em> are exclusively found in freshwater lakes in the lowlands and the mountain regions, supporting their indicator value for freshwater conditions. Our results provide a detailed examination of lake systems in modern conditions within highly climate-sensitive lowland and mountain permafrost landscapes.