The southern Balkans is located at the juncture between the west–east and north–south contrasting hydroclimatic domains across the Mediterranean, and this study focuses on diatoms as indicators of late Quaternary climate change and recent human impact in Lakes Dojran and Ohrid. Lake Dojran (Macedonia/Greece) is a shallow and currently hypereutrophic lake controlled by a classic Mediterranean climate. The Lake Dojran diatom data provide a new insight into changes in lake level and trophic status during the Younger Dryas and Holocene in the northeastern Mediterranean region, and are also important in disentangling regional climate effects from local catchment dynamics during the Holocene. The pigment data from the upper part of the sequence provide clear evidence for accelerated eutrophication of Lake Dojran due to water abstraction and intensified agriculture during the recent several centuries. Ancient lakes in Europe are restricted to the southern Balkan region, and Lake Ohrid (Macedonia/Albania), under the influence of Mediterranean and somewhat continental climates, is a rare example with a high degree of biodiversity and endemism. In deep and highly oligotrophic Lake Ohrid, the diatom data provide a clear picture of Lateglacial and Holocene changes in temperature and lake productivity which is primarily modulated through stratification or mixing regime and associated nutrient redistribution in the water column, and comparison with the data from Lake Dojran reveals different responses of diatoms to climate in the contrasting types of lakes. Diatom analysis of a short core in the southeastern part of Lake Ohrid reveals human‐induced eutrophication of Lake Ohrid in the recent several decades influenced by nutrient transfer through springs from hydraulically‐linked Lake Prespa. Preliminary diatom analysis of the ICDP deep core in Lake Ohrid generates a preliminary interpretation of the response of diatoms to glacial–interglacial cycles and the evolution of endemic diatom species during the past more than one million years
