Seydisuyu Basin, which contains very important agricultural areas and boron deposits of Turkey, is located in Eskişehir province. In this paper, the groundwater quality of Seydisuyu Basin was evaluated by using some physiochemical (temperature, conductivity, salinity, and demanded oxygen) and chemical (boron and arsenic) parameters. Groundwater samples were collected seasonally (2011-12) from 14 wells from the Seydisuyu Basin and all of the data obtained experimentally were compared with national and international drinking and usage water standards. Also, cluster analysis (CA) was applied to the results to classify the stations according to the contents of arsenic and boron levels by using the Past package program, factor analysis (FA) was applied to the results to classify the affective factors on groundwater 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 data, arsenic and boron accumulations of wells were higher than the drinking water limits specified by the Turkish Standards Institute (TS266), European Communities (EC), and World Health Organization (WHO) Drinking Water Standards. According to the results of FA, three effective factors that explain 76.36% of the total variance was detected and arsenic-boron contents of groundwater were positively loaded with the second factor, named as “Boron Works and Environmental Factor.” According to results of CA identified by using arsenic and boron accumulations, station 1, which was the closest well to the boron facility, showed the highest distance and lowest similarity with the other stations.