Microbial communities are the important components of lake ecosystems, and their structural and functional stability are crucial for the ecosystem functioning and service. Global changes characterized by nutrient enrichment and salinity increase have profound impacts on lake ecosystems, and it is important to reveal the mechanisms of how these factors affect the microbial community structure and stability. In this study, we conducted indoor simulation experiments with bacterioplankton communities under two nutrient levels and three salinity disturbance intensities (control, 3‰ and 9‰). We calculated four stability metrics such as reactivity, resistance, resilience and temporal stability, to explore the stability mechanisms of the communities. These metrics were based on the difference in cell density between the experimental groups and the control group at the same census. We also used high-throughput sequencing of bacterial 16S rRNA gene to analyze the community structure, and elucidated the responses of different bacterial groups to salinity disturbance under different nutrient levels. We found that the cell density and species richness of bacterioplankton decreased after salinity disturbance, and the relative abundance of salinity-sensitive groups decreased; the dissolved organic carbon in the water increased after salinity disturbance, which promoted the growth of other bacterioplankton adapted to the post-disturbance environment. Higher disturbance intensity significantly reduced the cell density, resulting in lower resistance; salinity disturbance and nutrient level had significant interactions on reactivity, resilience and temporal stability, and high nutrient level communities showed the lowest stability under 9‰ salinity disturbance. Most of the stability metrics showed significant positive correlations, which could jointly indicate the stability of planktonic bacterial communities. Resistance and resilience were not significantly correlated; thus, they could reflect the community stability from different perspectives. In summary, future nutrient enrichment and salinity increase of freshwater ecosystems will significantly reduce the stability of planktonic bacterial communities. The application of multiple stability indicators and high-frequency observation will help to understand the responses and stability mechanisms of bacterioplankton communities to disturbance.