Understanding and predicting the dynamic changes of microbial communities in source water reservoirs are crucial for ensuring water quality safety and ecological stability. However, the regime shifts mechanisms of microbial communities and their key driving factors remain systematically understudied. This study investigated the stability transition characteristics and driving factors of microbial communities through 16S rRNA high-throughput sequencing combined with environmental variable monitoring, while also predicting associated ecological functional shifts. The results revealed significant stability transitions in microbial communities, which could be categorized into two distinct states: State A, dominated by Cyanobacteria (posing a risk of cyanobacterial blooms), and State B, characterized by Bacteroidetes and other heterotrophic bacteria with strong capabilities in organic matter degradation and nitrogen cycling. Random forest analysis identified water temperature, ammonium nitrogen, and dissolved oxygen (DO) as primary environmental stressors driving stability transitions. FAPROTAX functional prediction analysis further demonstrated that microbial communities in State A exhibited enriched functions related to energy acquisition, whereas State B showed dominance in nitrogen cycling processes. This indicates that stability transitions involve not only shifts in species composition but also substantial reorganization of ecological functions. Importantly, short-term fluctuations in water temperature and dissolved oxygen directly influenced microbial community stability, triggering rapid ecosystem structural reorganization. This research elucidates the rapid stability transition mechanisms of microbial communities in oligotrophic reservoirs under environmental stress, advancing the theoretical framework of microbial ecosystem stability. It also provides a scientific basis for optimizing water quality management strategies in source water sources.