The individual or combined effect of water temperature and silicate on seasonal shift of dominant diatom species in a drinking water reservoir in China was studied in this paper. These effects were analyzed based on the field investigation of temporal dynamics in species composition and abundance of phytoplankton and environmental factors from September 2015 to August 2016. We firstly found that six dominant diatom species (Fragilaria nanana, Achnanthidium catenatum, Aulacoseira ambigua, Ulnaria ulna, Cyclotella meneghiniana and Asterionella formosa (Class Bacillariophyceae)), which accounted for 98.7% of the total abundance of diatoms and 46.8% of the total abundance of phytoplankton, showed an obvious seasonal succession. Then significant driving factors for seasonal shift of the dominant diatom species were selected by Redundancy Analysis. The result showed that water temperature and silicate were the main environmental factors affecting the growth of diatoms on temporal scales. Next, the regressions of water temperature and silicate and dominant diatom abundance were fitted in Generalized Additive Model separately, and the smoothers of water temperature and diatom species suggested that the dominant diatom species adapted to different optimum temperature ranges, which corresponded with the growth of seasonal changes. A positive linear correlation between silicate and diatom abundance was generated by Generalized Additive Model. Finally, the ordinal controls of water temperature and silicate on the growth of diatoms were analyzed on temporal scales specifically. We suggested that water temperature and silicate controlling the growth of diatoms in order. Diatoms grow well only when the two controlling factors simultaneously satisfy the growth conditions; as limiting factors, the two factors played their respective limiting roles in turn on temporal scales.