[Objective] To reveal the dynamics of bacterial communities in surface water and groundwater in the densely populated area of the Jianghan Plain across seasons and explore the underlying factors causing the temporal variations. [Methods] Water samples were collected from both surface water and groundwater in the densely populated area of the Jianghan Plain, and metagenomic sequencing was employed to investigate the seasonal variations of bacterial communities. The variations in environmental factors, bacterial community structure, and bacterial community assembly processes in the surface water and groundwater were compared considering rainy and dry seasons. [Results] For the surface water, the salinity (P < 0.01) and conductivity (P < 0.01) during the rainy season were lower than those during the dry season, while no significant seasonal variation was observed in turbidity. For the groundwater, the turbidity was higher in the rainy season than in the dry season (P < 0.05), while neither salinity nor conductivity showcased seasonal variations. The Shannon index of bacteria in the surface water in the rainy season was higher than that in the dry season (P < 0.01), whereas that in the groundwater presented no significant seasonal difference. The principal coordinates analysis and permutational multivariate analysis of variance (P=0.001) revealed significant seasonal variations in bacterial communities between surface water and groundwater. The Mantel test showed no significant correlations between the bacterial community in the groundwater and environmental factors during the dry season, while other communities were significantly correlated with at least one environmental factor. The neutral community model, modified stochasticity ratio (MST), and β nearest taxon index all indicated that stochastic processes exerted stronger effects on the bacterial community in the surface water during the rainy season than during the dry season, and the trend was similar but not significant for the bacterial community in the groundwater. The migration rate of surface water was higher during the rainy season than during the dry season, whereas that of groundwater showed an opposite trend. (5) The seasonal variations in the diversity of antibiotic resistance genes exhibited a negative correlation with MST (ρ=−0.164, P=4.942E−2) in the surface water, whereas the correlation was positive in the groundwater (ρ=0.393, P=1.452E−6). [Conclusion] The temporal dynamics of bacterial communities in surface water and groundwater in the densely populated area of the Jianghan Plain showed notable differences. These differences can potentially be attributed to distinct basic properties between surface water and groundwater, frequent environmental disturbances during the rainy season, and water exchange processes between surface water and groundwater.