Elucidating the diversity patterns and assembly mechanisms of microbial communities is crucial for comprehending ecological processes and assessing biogeochemical cycles in the hyporheic zones of cold regions. The spatial and temporal diversity patterns and mechanisms governing these microbial communities are not yet well understood. Our study revealed that microbial richness decreased rapidly during the initial freezing period. However, it began to increase during the deep freezing period due to the role of cold-resistant microorganisms. Meanwhile, the diversity of microorganisms showed a trend that was in line with the lake water- groundwater changes in temperature. Achromobacter and Crenothrix have been designated as biomarkers for the initial freezing period and deep freezing period, respectively. In these phases, factors such as dispersal limitation (26.8 %-47.6 %) and drift (15.1 %-45.2 %), along with other random factors, are the primary drivers of bacterial community assembly. Physical properties (pH, T, DO, EC, Eh) have been identified as the predominant factors (r = 0.75, p < 0.01) affecting the progression of community succession in hyporheic systems throughout the freeze-thaw cycles. Conversely, nutrient properties (r = 0.36, p < 0.01) and the presence of heavy metals (r = 0.18, p < 0.01) play lesser roles, influencing community composition according to partial least squares path modeling. Our insights significantly enhance the understanding of microbial communities in the HZ of frigid areas and carry important consequences for the stewardship and safeguarding of lacustrine ecosystems.