Statistical applications have been used to evaluate ecosystem quality in recent years. Factor analysis (FA) is a powerful multivariate statistical technique widely used to evaluate environmental pollution. Seydisuyu Stream Basin is located in the Central Anatolia Region of Turkey and it is one of the most important branches of the Sakarya River. There is a globally important boron mine on the basin and the system is exposed to intensive agricultural, domestic, and industrial pollution. The aim of this study is to evaluate the sediment quality of Seydisuyu Stream Basin using FA. For this purpose, some micro and macro element accumulations including Cr, Ni, Cu, Zn, As, B, Pb, Fe, K, Mn, and Mg in sediment were investigated by collected samples on the basin from 15 stations (including 3 from Çatören Dam Lake and 2 from the Kunduzlar Dam Lake) in summer 2012. According to FA results, three factors explained 90.95% of the total variance. The first factor (F1), the “urban-industrial factor,” explained 47% of total variance; the second factor (F2), the “agricultural factor,” explained 28.31% of total variance; and the third factor (F3), named the “geological-mining factor,” explained 15.63% of total variance.