Benthic algal flora of Karagol Lake, its seasonal variation, and the physical and chemical parameters of the water were studied between October 2008 and September 2010. The algal flora consisted of 112 taxa belonging to the divisions Charophyta (41), Chlorophyta (33), Cyanobacteria (18), Euglenozoa (17), Miozoa (2), and Ochrophyta (1). Six desmid taxa found in this research are new records for the freshwater algal flora of Turkey. The qualitative dominance of benthic taxa typical of slightly alkaline and mesotrophic ecosystems was observed. The qualitative and seasonal variations in epipelic taxa analyzed were dependent on the physicochemical characteristics of the water. Water quality was analyzed on the basis of benthic taxa, which are bioindicators. The physicochemical properties of the water are suitable for the development of a rich algal flora (especially desmids). According to the benthic algal composition and indicator species, it is estimated that Karagol Lake has mesotrophic lake characteristics. This is the first study of benthic algal flora of Karagol Lake and marks a significant contribution to the knowledge of Karagol-Sahara National Park's aquatic biodiversity.