Rebun Island is a key research area for the Baikal-Hokkaido Archaeology Project to better understand the dynamics of the Neolithic hunter-gatherers in the NW Pacific region. Hence, the ca. 19.5 m sediment core RK12 spanning the last ca. 16.6 cal. kyr BP was obtained from Lake Kushu. Our aim is to test its potential as a high-resolution multi-proxy archive. Here, we used diatoms to investigate the modern ecosystem of Lake Kushu and its surrounding area on Rebun Island and of Hime-numa Pond on Rishiri Island and selected core samples for comparison. Modern diatom and stable isotope analyses show well-mixed freshwater bodies with eutrophic, alkaline conditions. The fossil diatom and geochemical sediment analyses display three phases that represent major changes in the lake development: (i) a marshy phase (ca. 16.6-10 cal. kyr BP); (ii) a brackish water lagoon phase (ca. 10-6.6 cal. kyr BP); and (iii) a freshwater lake phase (since ca. 6.6 cal. kyr BP). This shows the major role of the post-glacial climate amelioration, global sea-level rise and marine transgression in the development of this landscape. Further analyses will provide a palaeolimnological record at (sub-)decadal resolution that will facilitate the interpretation of the hunter-gatherer dynamics.