Physico-chemical parameters, hydrological conditions, and microbial interactions can affect the growth and persistence of cyanobacteria, but the interacting effects among these bloom-forming factors are still poorly known. This hampers our capacity to predict the occurrence of cyanobacterial bloom accurately. Here, we studied the relationship between temperature, N and P cycles, and the microbial community abundance and diversity at 0.5 m under the surface of West Lake (China) from January 21 to November 20, 2015, in order to better understand the key factors regulating temporal changes in the cyanobacterial community. Using high throughput sequencing of the 16S rRNA gene V3-V4 region, we studied the diversity and abundance of bacteria. In parallel, we measured physico-chemical parameters and followed the abundance of key genes involved in N fixation, denitrification, and nutrient uptake. Multivariate analyses suggest that P concentration and water temperature are the key factors controlling the outbreak of summer cyanobacterial bloom. RT-qPCR analyses of the bacterial community and measurements of the copy number of denitrification-related gene (nirK, nosZ, nirS) show that denitrification potential and denitrifying bacteria relative abundance (Pseudomonas and Bacillus) increased in concert with diazotrophic cyanobacterial genera (Anabaena, Nostoc, Aphanizomenon flos-aquae) and the common bloom-forming non-diazotrophic cyanobacterium genus Microcystis. The present study brings new insights on the complex interplay between physico-chemical parameters, heterotrophic bacterial community composition, nitrogen cycle, and cyanobacteria dominance in a eutrophic lake.