In the present study, diatom flora of Seydisuyu Stream Basin (Turkey) was investigated and the water quality of the system was evaluated in a statistical and biological view. Epipelic (EPP), epilithic (EPL) and epifitic (EPF) diatoms were seasonally collected from 12 stations in 2012 along the Seydisuyu Stream Basin and some physical and chemical water quality parameters (temperature, salinity, TDS, pH, ORP, conductivity, nitrate, nitrite and phosphate) were measured during the field and laboratory studies. Biological Diatom Index (IBD) was used to assess the water quality of the basin and some mono (Pearson Correlation Index and Matrixplot Distribution Diagrams) and multi (Cluster Analysis and Factor Analysis) statistical methods were applied to detected all physical, chemical and biological data. According to data observed, Seydisuyu Stream Basin has II. - III. Class water quality in terms of investigated water quality parameters (Turkish Regulations) and a total of 48 diatom species were recorded for the basin by counting a total of 22.229 valves. Cymbella lanceolata, Diatoma vulgare, Fragilaria construens, Hantzschia amphioxys, Meridion circulare, Navicula cincta, Neidium iridis, Navicula venata, Pinnularia brebissonii, Synedra acus and Surirella ovata were the most dominant species in the region. According to result of IBD, the investigated region was in a mesotrophic state and has a moderate water quality. According to results of Factor Analysis, 9 factors explained 81.29% of the total variance and according to results of Cluster Analysis, stational similarity coefficients were determined as IBD Indices (0.98) > Environmental Parameters (0.85) > Diatom Flora (0.77) respectively.