In this study, it was aimed to use diatoms as representatives of phytobenthos for estimating the ecological status in Upper Sakarya Basin. Samples were taken seasonally from ten stations from April 2015 to December 2015. Stations 1, 2, 3, 4, 5, 6 and 7 were selected from rivers, stations 8 and 9 were selected from ponds which form Sakarya Springs. Station 10 was located at the outlet of Cifteler Aquaculture and Research Station. Diatoms were identified, counted and 19 diatom indices were calculated. Moreover, water temperature, dissolved oxygen, pH, electrical conductivity were measured in situ, and total nitrogen, orthophosphate and alkalinity were analysed. Finally, ecological status was estimated by evaluating biological, chemical and hydromorphological status according to Water Framework Directive. In total, 96 diatom species were identified from samples and Achnanthidium minutissimum, Cymbella excisa, Craticula subminuscula and Fragilaria brevistriata were the dominant species. Among diatom indices, IDP index which shows a high correlation with total nitrogen was used for the evaluation of the biological status. As a result, ecological status of the station 2 was estimated as high (class I), the status of stations 1, 4, 7, 8, 9 and 10 was estimated as good (class II), and the status of stations 3, 5, 6 was estimated as moderate (class III).