Baisha River was chosen as a testing area in this research, and the similarities and differences were compared between diatom-based method and physico-chemical method in Chinese rivers at the present stage, besides, water ecological condition had also been assessed in Baisha River. The physico-chemical parameters showed that the water quality level of Baisha River is from Grade Ⅰ to worse than Grade V, while Specific Pollution Sensitivity Index (SPI) and Biotic Diatom Index (BDI) indicated that its water quality is from bad to high quality level. These two assessment results were almost identical as a whole although differences between them did occur. For diatom eco-type, the results showed that the first three sites are principally dominated by oligosaprobous and β-mesosaprobous, N-autotrophic, Polyoxybiontic taxa, and the fourth site (except Nov. 2010) is principally dominated by Meso-to polysaprobous, N-heterotrophic and low aerobic diatom taxa. All sites were dominated by circumneutral and alkaliphilous species in Baisha River. There were negative significant relationships between SPI, BDI and conductivity, total phosphorus, ammonia nitrogen, and chloride. In addition, there were also negative significant relationships between BDI and permanganate index, total nitrogen, nitrite nitrogen, and soluble phosphate. The results of the present study provide a good experience for biomonitoring in China, but more researches are needed in order to establish Chinese biomonitoring standard.