Benthic diatoms are the main component in many aquatic ecosystems such as streams, creeks and rivers, and they function as important primary producers and chemical modulators for other organisms in the ecosystems. In this study, the composition of benthic diatoms was investigated and further explored the primary physicals and chemicals affecting their temporal variations in the upper Han River, China. There were seasonal variations in physical and chemical variables in waters over the sampling period of 2007–2010. Water temperature (t), chemical oxygen demand, total nitrogen, dissolved organic carbon (DOC), silica and fluoride were much higher in the highflow season (i.e., July or August) than these in the base flow season. Three species Achnanthidium minutissimum (composed of 10.7 % of the total diatom abundance), Achnanthidium pyrenaicum (11.9 %), and Achnanthidium subatomus (12.7 %) accounting for more than 5 % of the total diatom abundance were persistently dominant in all seasons, while the other two prostrate and motile species including Eolimna minima and Nitzschia dissipata also dominant in the base flow season. The species richness always peaked in autumn with significant difference with summer (p<0.01), and density of benthic diatom varied and peaked in April. Analyses indicated that the temporal variation in benthic diatom communities was strongly related to, nitrogen, organic pollutants (indicated byCOD and DOC), and hydrological regime. The research will expand the understanding of water chemistry monitoring, and improve watershedscale management and conservation efforts in the upper Han River, China.