To gain insight into the variation of diatoms and silicon and their interaction in a tributary of the Three Gorges Reservoir (TGR), the Xiangxi River was chosen as a representative tributary, and dissolved silicon (DSi) and biogenic silicon (BSi) were investigated monthly from February 2015 to December 2016, accompanied by diatom species composition and cell density analyses. The results showed that the diatom population and its relationship with silicon concentration were significantly different between the lacustrine zone and riverine zone (P < 0.05). The cell density in the lacustrine zone (6.20 x 10(5) similar to 9.97 x 10(7) cells/L) was significantly higher than that in the riverine zone (7.90 x 10(4) similar to 1.81 x 10(7) cells/L) (P < 0.01). Water velocity was a key factor in determining the diatom species composition. Centric diatoms were the dominant species in the lacustrine zone, and pennate diatoms were the primary species in the riverine zone, which indicated that centric diatoms outcompete pennate diatoms under the influence of the TGR's operation. BSi showed a significant linear relationship with the cell density. DSi had a significant negative relationship with the cell density in the lacustrine zone, while no significant relationship was found in the riverine zone. This meant that the main contributor to BSi was diatoms, but DSi was primarily affected by water discharge, not diatom uptake. It could be deduced that the spatiotemporal heterogeneity of diatom communities was influenced by the TGR's operation. Silicon cycling in the tributary was significantly affected by diatoms, and the current concentration of DSi was sufficient for diatom growth and showed no significant effects on the diatom community.