Rwenzori Mountains National Park, which straddles the border between the Democratic Republic of Congo and Uganda, has experienced rapid glacier loss since the beginning of the twentieth century, yet there has been little investigation of aquatic biodiversity change in the park. This study presents a paleolimnological analysis from Lake Mahoma (2990 m asl), which is situated in the bamboo-forest transition zone. Diatom and organic geochemistry data from a 39-cm-long sediment core with a basal age of c. 1715 CE were compared with new analyses of previously published data from Lakes Bujuku (3891 m asl) and Lower Kitandara (3989 m asl), in the alpine zone. Comparisons were made to determine if aquatic ecosystem changes exhibited similar inter-lake patterns over the past ~ 150 years of climate warming and glacial recession, or if only local change was apparent. The diatom flora of Lake Mahoma is acidophilous, dominated by Aulacoseira ikapoënsis since at least the mid eighteenth century. In recent decades, the obligate nitrogen-heterotroph Nitzschia palea increased in importance, concurrent with declining δ15Norg values. We suggest that these late twentieth century changes were linked to regional warming and increased thermal stratification of Lake Mahoma. Regional comparisons of the Rwenzori lakes were done using existing organic geochemistry records (total organic carbon, C/N and δ13Corg) and through diatom compositional turnover analyses, and categorisation of species into one of four diatom growth morphology traits, or guilds: tychoplanktonic, high-profile, low-profile and motile. Over the past 150 years, all three lakes showed unidirectional, compositional diatom turnover, indicating that deterministic processes had affected diatom communities. Declining turnover at each site is broadly mirrored by an increase in tychoplanktonic taxa, along with concomitant declines in high-profile diatoms at Lake Mahoma, and low-profile diatoms at Lake Bujuku, and at least for the past 60 years, at Lower Kitandara. The interplay between diatom guilds at all sites is mainly a consequence of competition for available resources. Sediment organic carbon at all sites comes from both autochthonous and allochthonous sources, the relative abundances of which are influenced by the time elapsed since lakes had glaciers in their catchment
