A thermokarst lake sediment core from the centre of Herschel Island was analysed in order to reconstruct post-glacial palaeoenvironmental changes and landscape dynamics in this part of the Western Canadian Arctic. The ice-rich island in the Southern Beaufort Sea is of outstanding scientific interest since it archives the northernmost terrestrial lake record of the Yukon Territory. Besides previously published sedimentological and biogeochemical analyses, we applied micropaleontology and hydrochemistry on pore waters. The formation of the lake occurred during the Holocene Thermal Maximum, around 11.5 to 10.0 cal ka BP. Here, brackish shallow water ostracods (Heterocyprideis sorbyana) and foraminifers (Cribroelphidium excavatum) prevailed and electrical conductivity of pore waters of approximately 13,000 µS/cm demonstrates a marine influence. Reworking from older sediments, however, cannot be ruled out completely. The lake development until about 7.0 cal ka BP was associated with a period of intense thermokarst activity and the pollen-based temperature reconstruction shows that TJuly was greater than 8°C during the early Holocene at the initial stage of Lake Herschel. The freshwater ostracod Cytherissa lacustris was the dominant species. Pollen concentrations and influx were low prior to 6.0 cal ka BP and subsequently increased, especially in the past thousand years. The ostracod association became more diverse in the Mid-Holocene; Fabaeformiscandona levanderi is the dominant species besides C. lacustris. The reconstructed TJuly were lower from 7.0 to 5.5 cal ka BP and relatively high but variable until 1.8 cal ka BP. Pollen of Cyperaceae and Poaceae were generally the most abundant taxa. However, Poaceae pollen increased in sediments younger than 3.0 cal ka BP and Cyperaceae pollen decreased after 1.8 cal ka BP. Pollen from several shrubs were found in relatively high quantities, including Alnus, Juniperus and Betula; only the latter is found in the recent tundra environment. The ostracod associations show a persistent lake with high input of allochthonous material and possibly elevated salinity. A change in the sedimentation rate between 1.8 to 0.9 cal ka BP is explained either by a hiatus due to modified drainage conditions or slumping. Bioproductivity increased, as shown by a richer fauna (Chironomidae). Foraminifers are abundant and occur together with fresh and brackish water ostracods reflecting elevated salinity. The change of facies is also recorded in pore waters chemistry characterized by lower pH values, slightly higher electrical conductivity and increased Ca, Mg, Mn, Sr and SO4 ion content. The final late-Holocene phase, beginning by 0.9 cal ka BP, was characterized by an elevated and variable NO3 ion content in pore waters, a poorer ostracod fauna and disappearance of foraminifers, as well as pollen-based TJuly below 7°C.