Abstract: To evaluate the condition of the Wei River Basin, 60 sampling sites were selected to investigate the diatom community structure during the wet season (October 2012) and the dry season (April 2013). A total of 221 species of diatom were identified in the wet season and 148 species were observed in the dry season. On the basis of the Multi-Response Permutation Procedures (MRPP), the diatom community structure showed a significant difference between the Wei River, Jing River and Beiluo River. The species richness, Shannon-Wiener diversity and evenness in the wet season (Wei River:30,3.05,0.63; Beiluo River:37,3.42,0.66) were significantly higher than those in the dry season (Wei River:23,2.11,0.46; Beiluo River:23,2.52,0.56). However, the metrics of diatom were similar in both seasons for the Jing River. According to Canonical Correspondence Analysis (CCA), the results showed that flux, suspended solids and the total dissolved solids were the main factors affecting the community structure of diatom in the wet season in the Wei River, Jing River, and Beiluo River, respectively, while ammonia, suspended solids and hardness were the main factors in the dry season. An assessment of river condition was made using the Diatom Index of Biological Integrity (D-IBI) and Biological Diatom Index (BDI) in different seasons. The results in both seasons showed that the condition of the Wei River Basin was fair. The health condition in the upstream and the right bank branch of the Wei River was excellent, as was the upstream of the Jing River and the midstream of the Beiluo River, whereas the downstream of the Wei River, the middle and downstream of the Jing River and headwater of the Beiluo River were poor.