In the present study, water quality of Seydisuyu Stream Basin were investigated by determining temperature, conductivity, salinity, TDS (total dissolved solid), pH, ORP (oxidation-reduction potential), dissolved oxygen, nitrate (NO₃), nitrite (NO₂), orthophosphate (PO₄), sulphate (SO₄), COD (chemical oxygen demand), BOD (biological oxygen demand), calcium, magnesium, sodium, potassium, arsenic, and boron parameters seasonally in 2012 at 15 stations. All the data obtained were compared with 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). Some mono (one-way ANOVA test, Pearson Correlation Index) and multi (factor and cluster analysis) statistical techniques were used to evaluate the data properly. Also, the ArcGIS package program was used to make distribution maps of arsenic and boron in order to provide visual summaries of these elements’ accumulation in the basin. According to the results of FA, four factors named as “Nutrient,” “Agricultural,” “Boron,” and “pH” explained 77.4% of the total variance, and according to the results of CA, three statistically significant clusters, named “Low,” “Moderate,” and “High” polluted areas were formed. In a macroscopic point of view, Seydisuyu Stream Basin has class IV water quality in terms of boron; downstream of the basin has class II, upstream has class III water quality in terms of arsenic. It was also determined that arsenic and boron concentrations in Seydisuyu Stream Basin water were much higher than the drinking water limits.