The Weishan Lake serves as a crucial reservoir and regulating lake in the Eastern Route of the South-to-North Water Diversion Project and the ecological health of its lake ecosystem directly impacts the water quality for water diversion. Diatoms are particularly sensitive to changes in water environments, and the composition of diatom communities serves as a significant indicator of the health of aquatic ecosystems. To understand the composition of diatom communities in Weishan Lake and their relationship with environmental factors, thereby providing scientific grounds for the protection of the lake’s ecological environment, surface sediment diatoms, water samples, and sediments were collected and analyzed. The study revealed that there are 64 species from 19 genera of diatoms in Weishan Lake, predominantly comprising epiphytic and planktonic species. Dominant species include Fragilaria brevistriata, Achnanthes minutissima, and Stephanodiscus parvus, indicating an overall meso-eutrophic status. According to the diatom composition and biodiversity index, the diatom community was divided into three combination zones. Redundancy analysis (RDA) results indicated that the water environmental factors influencing the composition and distribution of diatom communities in Weishan Lake are TP, TOC, DO, NO2 −–N, and Ca2+, collectively explaining 35.60% of the variation in diatom community composition. Due to the influence of agricultural and industrial wastewater runoff, domestic sewage discharge, and cage aquaculture, Weishan Lake is in a mesotrophic eutrophication state. Therefore, it is recommended that strict control over inappropriate human activities in the lake area be implemented in the future to ensure the safety of water quality for water diversion.