Seydisuyu Stream Basin, known to be exposed to agricultural and domestic pollution, is one of the most important branches of the Sakarya River. In addition to the geologic structure of the basin, Kirka Boron Mine is one of the most important inorganic pollution sources for the system and also for the Sakarya River. In this study, the water quality of Seydisuyu Stream was evaluated by determining some physiochemical (temperature, conductivity, salinity, TDS, pH, ORP, dissolved oxygen, and nitrate) and chemical (boron and arsenic) parameters. Water samples were collected an average of 10 times per month between September 2011-September 2012 from Hamidiye Village, located at the downside of Seydisuyu Stream. All of the data obtained experimentally were compared according to the criteria of SKKY (Water Pollution Control Regulation in Turkey) and evaluated as drinking water according to the criteria of TS266 (Turkish Standards Institute), EC (European Communities), and WHO (World Health Organization). Cluster analysis (CA) was applied to the results to classify the seasons according to water quality by using the Past package program. Factor analysis (FA) was applied to the results to classify the affective factors on water quality, and Pearson Correlation Index was applied to the results to determine the relations of parameters by using the SPSS 17 package program. According to the results of FA, four factors explained 84.78% of the total variance and according to the results of CA, three statistically significant clusters were formed. In a macroscopic view, the monitoring station has class I-II water quality in terms of arsenic and class IV water quality in terms of boron. It was also determine that arsenic and boron accumulations in Seydisuyu Stream water were much higher than drinking water limits.