Ancient lakes, which are important centres of biodiversity and endemism, are threatened by a wide variety of human impacts. To assess environmental impact on ancient Lake Ohrid we have taken short sediment cores from two contrasting site locations, comprising a site of urban pollution and an apparently pristine area. Recent impacts on water quality and ecology were assessed using sediment, geochemical, ostracode, and diatom data derived from analysis of two 210 Pb-dated sediment cores spanning the period from 1918 to 2009. According to the index of geoaccumulation, sediments were often moderately contaminated with As. Fe and Ni concentrations often exceeded reported maximum limits above which harmful effects on sediment-dwelling organisms are expected. Productivity in the (pristine) south-eastern part of Lake Ohrid (Sveti Naum) is generally lower than in the north, probably due to the strong influence of spring discharge. Low ostracode and diatom concentrations, low abundance of the epilimnetic diatom Cyclotella ocellata, and low values of TOC and TIC indicate a lower productivity from the early 1920s to the late 1980s. Since the mid 1970s, increased relative abundance of C. ocellata and increasing diatom concentration indicate increasing productivity in the south-eastern part. Rising numbers of ostracode valves and higher TIC and TOC contents in both sediment cores indicate an increase in productivity during the late 1980s. A slight increase in productivity near Sveti Naum continued from the early 1990s until 2009, witnessed by rising TC, TIC, and TOC content and a generally high number of ostracode valves and ostracode diversity. The area near the City of Struga (site of urban pollution) is also characterized by rising TOC and TIC contents and, furthermore, by increasing Cu, Fe, Pb, and Zn concentrations since the early 1990s. The recent reduction in the number of ostracode valves and ostracode diversity is probably caused by a higher heavy metal load into the lake. This suggests that living conditions for the endemic species in Lake Ohrid have become less favourable in the northern part of the lake, which might threaten the unique flora and fauna of Lake Ohrid.Keywords (separated by '-') Lake Ohrid -Palaeolimnology -Eutrophication -Geochemistry -Ostracodes -DiatomsFootnote Information Electronic supplementary material The online version of this article