Seasonal ice cover is a critical ecohydrological variable governing the structure and function of cold-region lakes. However, a mechanistic understanding of its impact on microbial-mediated biogeochemical cycles has been lacking, hindering effective management. This study employs an integrated ecohydrological approach, combining ​metagenomic sequencing and multidimensional bioinformatics with ice–water–sediment field observation, to quantitatively decipher how freezing drives the succession of bacterial communities and nitrogen metabolism across media in a shallow lake from a cold-arid region. The key findings and management implications include the following: Bacterial richness and diversity were significantly higher during ice cover than during the ice-free period, with water column communities exhibiting consistently higher diversity than that in sediment. Ice cover markedly reshaped water bacterial community structure but had limited effects on sediment communities. Freezing strongly influenced nitrogen metabolism: in sediment, ammonia assimilation, mineralization, and nitrification dominated but varied seasonally, while the nitrogen fixation potential dropped sharply (≈4× higher in ice-free conditions). Water column nitrogen transformation pathways (e.g., ammonia assimilation, mineralization, assimilatory nitrate reduction) were significantly suppressed under ice. Community assembly was primarily governed by stochastic processes, with ice cover shifting the dominant stochastic mechanism from drift to dispersal limitation. Heterogeneous selection emerged as a key deterministic driver. This study underscores the critical role of ice cover as an ecohydrological driver shaping microbial structure and function in seasonally frozen lakes. By linking freezing-induced hydrological changes to bacterial ecological processes, our work offers a novel biohydrological indicator for lake conservation under climate change and provides a mechanistic basis for predicting ecological risks and guiding management strategies in cold-region shallow lakes.