Hydrological Connectivity and Aquifer Permeability Regulate Microbial Assembly and Nitrogen Transformations in a Lake‐Groundwater System

Lake‐groundwater systems are characterized by pronounced seasonal recharge dynamics and nutrient accumulation within low‐permeability aquifers. Microbial communities mediate nitrogen transformations in these heterogeneous systems, yet their spatiotemporal dynamics and responses to the groundwater flow regimes remain largely unresolved. In this study, the evolution of groundwater microbial communities was investigated across contrasting recharge zones in the Poyang Lake area, one of China's largest lake‐groundwater systems, during dry and wet seasons. The discharge area with the low‐permeability aquifer was enriched with NH 4 + ‐N, Fe 2+ , and total organic carbon (TOC), exhibited lower oxidation‐reduction potential (ORP), and showed limited seasonal variability across seasons compared with other aquifers experiencing stronger hydrological seasonality. Despite the hydrochemical stability, microbial communities in the low‐permeability aquifer displayed greater dry‐to‐wet seasonal shifts, suggesting a heightened biological sensitivity to even subtle hydrological variations. From dry to wet season, denitrification potential decreased, whereas nitrogen fixation potential increased, with the strongest shifts occurring in the low‐permeability aquifer. Although microbial communities in this aquifer were associated with Fe 2+ , NH 4 + ‐N, and ORP, these variables independently explained only a small proportion of the total variance (<8%). Intriguingly, community assembly was primarily stochastic, with stronger drift in the low‐permeability aquifer, indicating environmental‐microbial decoupling. Microbial source tracking analysis suggested that microbial communities in the discharge area were largely associated with upstream groundwater with additional potential contributions from lake‐groundwater exchange, which may reflect delayed recharge signatures. These findings suggest that hydrological dynamics, more than static chemistry, modulate variability of microbial community assembly and nitrogen‐cycling in groundwater.