Diversity and ecology in the diatoms of Sakarya River were investigated between October 2009 - September 2010. As a result, Navicula radiosa Katz was the dominant taxa at the first and fourth stations. Gomphonema olivaceum (Horrn.) Brebisson, Craticula cuspidata (Kutz.) D.G. Mann, Rhoicosphaenia abbreviata (C. Agardh) Lange-Bertalot, and Nitzschia recta Hantzsch ex Rabenhorst taxa were found to be widespread throughout the research. Significant correlation was identified between SI and DI-CH and between TI and DI-CH in the epilithic diatoms. The minimum correlation was identified between SI and TI. Based on the assessments, according to Si, the fourth station was classified as 11-Ill quality class, or critically polluted. Other stations were classified as 11 quality class, or moderately polluted. According to T1, the first station was determined to be II-Ill (mesotroph-eutroph) quality class. Second, third and fourth stations were found to be III (polytroph) quality class. According to DI-CH, the fourth station was classified as quality class IV (moderately polluted), while the first, second and third stations were determined as III (less polluted) quality class.