EM‐induced bio‐clogging: Formation evolution and permeability response under variably saturated flow

The vadose zone is an important yet frequently understudied environment where bio‐clogging occurs during managed aquifer recharge. Understanding the synergistic effects of key hydrodynamic factors—water content ( θ ) and flow velocity (V)—on biofilm development and permeability reduction is essential for predicting and mitigating clogging. This study uses an effective microorganisms (EM) consortium to elucidate bio‐clogging mechanisms under variably saturated flow. Static batch experiments revealed that carbon source availability and temperature positively regulate EM growth and extracellular polymeric substance (EPS) secretion. Soil column experiments demonstrated that unsaturated conditions were found to promote higher microbial activity and organic accumulation compared to saturated groups, inducing more significant permeability decay. While high flow rates enhanced bacterial migration (84.3% breakthrough in saturated columns), unsaturated conditions effectively suppressed microbial mobility. The synergistic pore occlusion by EPS and bacterial cells was identified as the primary clogging mechanism. Permeability evolution exhibited distinct triphasic characteristics: a rapid initial decline, a mid‐term stabilization, and a long‐term dynamic equilibrium at approximately 4.3% of the initial conductivity. This quantitative threshold provides a core reference for clogging risk early warning, segmented hydrodynamic regulation strategy formulation, and operation cycle optimization of soil aquifer treatment (SAT) systems for agricultural drainage recharge in the Sanjiang Plain and similar rice‐growing areas. This study reveals a stratified clogging mechanism—bacteria‐dominated near the surface and EPS‐dominated in deeper layers—governed by θ ‐V synergism. Our findings offer a reference framework for optimizing the operation of recharge systems and developing targeted anti‐clogging strategies in the vadose zone.