Quasi-3D Numerical Modeling of Groundwater Flow, Particle Transport, and Clogging-Induced Interlayer Leakage in Heterogeneous Multilayer Aquifers

Physical clogging during managed aquifer recharge can reduce aquifer conductivity and alter leakage across intervening aquitards. This study presents a quasi-three-dimensional model coupling horizontal groundwater flow, suspended-particle transport, retention, porosity and conductivity change, and clogging-sensitive interlayer exchange in three heterogeneous aquifer units separated by two unresolved aquitards. Simulations start from the clean steady solution to isolate clogging effects from hydraulic redistribution. Flow is solved using an alternating-direction implicit scheme, while particle transport and retention use conservative advection–dispersion and positivity-preserving reaction steps. Verification is separated by level: the flow solver is second-order accurate in space against an exact solution (observed order 2.009), whereas the formally first-order coupled system, which has no analytical solution, is assessed through conservation, positivity, datum invariance, and grid/time refinement. After 200 days, mean conductivity in the recharge unit decreases by 1.038%. Relative to a matched clean-interface control, interface clogging changes mean interlayer leakage by −0.0528% and −0.0451%, a numerically resolved but physically very small effect. Sensitivity tests show that heterogeneity and constitutive assumptions affect response magnitude. These results are conditional on the synthetic parameter set and require calibration and independent physical validation before predictive use.