In this study which is the first attempt to systematically identify algae of eighteen freshwater high mountain glacier lakes ecosystems were investigated. Samples were gathered from the lakes between August 2011 and October 2012. Secondly, some parameters of physical and chemical water quality (such as temperature, dissolved oxygen, pH, and electricity conductivity) were measured with the field and laboratory studies, so as to determine the water qualities of lakes. In particular, pH has not exceeded 7.06 in all lakes throughout the year. Physical, chemical and biological data were examined with cluster analysis, in order to categorize different characteristics of the lakes. According to data, 58 Bacillariophyta, 17 Chlorophyta, 15 Cyanobacteria, 2 Euglenophyta, 2 Pyrrophyta, and 2 Cryptophyta species were classified in total with the planktonic and benthic samples from the investigation of eighteen freshwater lakes.