The main goal of this study is to determine the composition, diversity and ecology of benthic diatoms in Karagol Lake in Karagol-Sahara National Park. Monthly sampling (from sediments, stones and aquatic plants in littoral zone of the lake) taken in three consecutive years revealed 57 diatom taxa with Gomphonema and Pinnularia being the most abundant species while other genera are represented with three or fewer species. Lindavia ocellata was the most dominant taxon in the samplings examined throughout the whole study. The values of diversity and evenness indices are high during the spring and early summer. Based on cluster analysis for monthly samples of epipelic diatom, there are two different groups at the lowest similarity level. The associations between August 2010 and September 2010 months are the most significant with 86.02%. The organism number of epipelic diatoms showed positive correlation (P<0.01) with dissolved oxygen, while negative correlation (P<0.05) with temperature. Detailed floristic and ecological examination of the benthic diatom communities has not been carried out before this study in this lake. Therefore, this study is the first to our knowledge towards revealing aquatic benthic diatom biodiversity of Karagol-Sahara National Park and provides basis for future investigations.