The effects of thirteen water quality parameters(Conductivity, pH, Dissolved Oxygen, Biochemistry Oxygen Demand, Chemistry Oxygen Demand, Total Nitrogen, NH₄-N, NO₃-N, NO₂-N, Total Phosphorus, PO₄-P, SiO₂ and Cl) on the distribution of epilithic diatoms in the Dongjiang basin were investigated by correlation analysis (CA), canonical correspondence analysis (CCA) and weighted average (WA). Correlation analysis showed that NH₄-N, NO₂-N, PO₄-P, Cl, DO and BOD₅ had significant correlations with the other seven water quality parameters, while CCA analysis revealed that the impacts level of the five environmental variables. Cond., COD_KMnO4, NO₃-N, TN and TP on the variation in community composition of epilithic diatoms were in the order of Cond.> NO₃-N > COD_KMnO4 > TP > TN. Furthermore, the optimum ecological values of Cond., NO₃-N, COD_KMnO4, TP and TN for epilithic diatoms were calculated using weighted average regression method to be 39.20-642.00μs/cm, 0.46-2.77mg/L, 1.0-5.5mg/L, 0.02-0.64 mg/L and 0.48-3.43mg/L, respectively. The results indicated that Cond., COD_KMnO4, NO₃-N, TN and TP were the major water quality parameters affecting the distribution of diatom assemblages. Cyclostephanos invisitatus, Nitzschia acicularis, N. capitellata and N. intermedia could be used as bioindicators for the higher conductivity in the Dongjiang river basin. Aulacoseira ambigua, A. lirata, Cyclotella meneghiniana, Cyclostephanos invisitatus, Eunotia minor, Nitzschia acicularis, N. clausii and Pinnularia subcapitata were indicative species for TN and TP in the Dongjiang river basin. Moreover, Nitzschia acicularis is the best bioindicator for TN and TP in the Dongjiang basin, while Navicula eidrigiana is the least sensitive bioindicator for TN and TP.